Gene database tables: Orthologs, Genes under selection, DEGs and RNAi

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Last updated: 2025-05-05

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Knit directory: locust-comparative-genomics/

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/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data	data
/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca	data/orthofinder/Schistocerca
/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera	data/orthofinder/Polyneoptera

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    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cancellata/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_results_sva_Head_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_results_sva_Head_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_sigresults_sva_Head_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/DESeq2_sigresults_sva_Head_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV2_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_scatter_SV2_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_results_sva_Thorax_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_results_sva_Thorax_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_sigresults_sva_Thorax_cubense.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/DESeq2_sigresults_sva_Thorax_cubense_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/cubense/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_sva_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_results_sva_Head_gregaria_togregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_sva_Head_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/DESeq2_sigresults_sva_Head_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV3_Head_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Head/sva_stripchart_SV4_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/PCA_labelled_VST_togregaria.png
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_Thorax_gregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_sva_Thorax_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_results_sva_Thorax_gregaria_togregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_Thorax_gregaria.csv
    Deleted:    data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_sva_Thorax_gregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/DESeq2_sigresults_sva_Thorax_gregaria_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/gregaria/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_results_sva_Head_nitens.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_results_sva_Head_nitens_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_sigresults_sva_Head_nitens.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/DESeq2_sigresults_sva_Head_nitens_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV2_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_scatter_SV2_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/nitens/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_results_sva_Head_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_results_sva_Head_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_sigresults_sva_Head_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/DESeq2_sigresults_sva_Head_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/MA_plot_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/MA_plot_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_VST_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_VST_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_labelled_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_normTransform_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_normTransform_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_rlog_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/PCA_rlog_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_VST_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_VST_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_normTransform_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_normTransform_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_rlog_Head.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/heatmap_rlog_Head_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_scatter_SV1_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV1_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV1_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV2_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV2_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV3_Head.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/sva_stripchart_SV3_Head_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/volcano_DEG_Head_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Head/volcano_DEG_Head_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/PCA_labelled_VST.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/PCA_labelled_VST_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_results_sva_Thorax_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_results_sva_Thorax_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_sigresults_sva_Thorax_piceifrons.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/DESeq2_sigresults_sva_Thorax_piceifrons_togregaria.csv
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/MA_plot_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/MA_plot_DEG_Thorax_igris_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_VST_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_VST_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_labelled_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_normTransform_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_normTransform_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_rlog_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/PCA_rlog_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_VST_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_VST_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_normTransform_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_normTransform_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_rlog_Thorax.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/heatmap_rlog_Thorax_togregaria.pdf
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV1_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV2_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_scatter_SV2_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV1_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV1_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV2_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV2_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV3_Thorax.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/sva_stripchart_SV3_Thorax_togregaria.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/volcano_DEG_Thorax_igris.png
    Modified:   data/DEG_results/Bulk_RNAseq/piceifrons/Thorax/volcano_DEG_Thorax_igris_togregaria.png
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_americana.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_americana_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cancellata.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cancellata_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cubense.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_cubense_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_gregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_gregaria_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_nitens.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_nitens_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_piceifrons.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Head_piceifrons_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_americana.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_americana_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cancellata.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cancellata_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cubense.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_cubense_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_gregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_gregaria_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_nitens.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_nitens_togregaria.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_piceifrons.csv
    Modified:   data/WGCNA/input/Bulk_RNAseq/datExpr_Thorax_piceifrons_togregaria.csv
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesprotein_Schisto_Jan2025.txt
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesproteinbiotype_13species_Jan2025.csv
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_A. simplex.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_B. rossius.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_C. secundus.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_D. australis.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. bimaculatus.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. longicornis.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_P. americana.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_americana.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cancellata.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cubense.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_gregaria.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_nitens.pdf
    Modified:   data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_piceifrons.pdf
    Deleted:    data/orthofinder/Polyneoptera/Results_I2/SingleCopyOrthogroups_genesprotein_13species_Jan2025.txt
    Deleted:    data/orthofinder/Schistocerca/Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_Jan2025.csv
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_americana.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cancellata.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cubense.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_gregaria.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_nitens.pdf
    Modified:   data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_piceifrons.pdf
    Deleted:    data/orthofinder/Schistocerca/Results_I2/SingleCopyOrthogroups_genesprotein_6species_Jan2025.txt
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_americana.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_cancellata.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_cubense.csv
    Modified:   data/overlap/Bulk_RNAseq/overlapping_genes_head_thorax_piceifrons.csv
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_americana.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_cancellata.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_cubense.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_piceifrons.png
    Deleted:    data/overlap/summaryPolyneoptera_DEGs_Orthogroups_Feb2025.csv
    Deleted:    data/overlap/summaryPolyneoptera_DEGs_Orthogroups_togregaria_Feb2025.csv
    Deleted:    data/overlap/summarySchistocerca_DEGs_Orthogroups_Feb2025.csv
    Deleted:    data/overlap/summarySchistocerca_DEGs_Orthogroups_togregaria_Feb2025.csv

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/3_compiling_tables.Rmd) and HTML (docs/3_compiling_tables.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	9451c02	Maeva TECHER	2025-03-03	adding GO enrich
html	9451c02	Maeva TECHER	2025-03-03	adding GO enrich
Rmd	3746422	Maeva TECHER	2025-02-12	Add RNAi
html	3746422	Maeva TECHER	2025-02-12	Add RNAi

---

Load the libraries

# Load necessary libraries
library(tidyr)          # Data transformation (pivot_wider)
library(readr)          # Efficient CSV reading/writing
library(stringr)        # String manipulation
library(purrr)          # Functional programming (handling missing files)
library(tibble)         # Improved dataframe handling
library(forcats)        # Factor manipulation (optional, if needed for ordering)
library(tidyverse)
library(kableExtra)
library(DT)
library(dplyr)          # Data manipulation


# Path for all species
workDir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data"
allspecies_path <- file.path(workDir, "/list/13polyneoptera_geneid_ncbi.csv")
allspecies_df <- read.table(allspecies_path, sep = ",", header = TRUE, quote = "", fill = TRUE, stringsAsFactors = FALSE)
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
species_order <- c( "nitens", "cubense", "americana",  "piceifrons", "cancellata", "gregaria")

1. Compiling orthologs and DEGs

Schistocerca-based

Inflation I2

STRATEGY 1: to gregaria

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_annotated_Jan2025.csv")
ortholog_df <- read.csv(input_file, header = TRUE, stringsAsFactors = FALSE)

# Replace NA values in the Orthogroup column with "Unassigned"
#ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
#if ("gene_id" %in% colnames(ortholog_df)) {
#    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
#}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    dplyr::distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,"_togregaria.csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,"_togregaria.csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_I2_DEGs_Orthogroups_togregaria_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

STRATEGY 2: to own RefSeq

This table summarize the DEGs as well as the orthogroups it belongs. Here

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)

# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,".csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,".csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_I2_DEGs_Orthogroups_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

Inflation I5

STRATEGY 1: to gregaria

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I5/Orthogroups_genesproteinbiotype_Schistocerca_annotated_Jan2025.csv")
ortholog_df <- read.csv(input_file, header = TRUE, stringsAsFactors = FALSE)

# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
#if ("gene_id" %in% colnames(ortholog_df)) {
#    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
#}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    dplyr::distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,"_togregaria.csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,"_togregaria.csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_I5_DEGs_Orthogroups_togregaria_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

STRATEGY 2: to own RefSeq

This table summarize the DEGs as well as the orthogroups it belongs. Here

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I5/Orthogroups_genesproteinbiotype_Schistocerca_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)

# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,".csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,".csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_I5_DEGs_Orthogroups_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

Polyneoptera-based

Inflation I2

STRATEGY 1: to gregaria

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.

library(tidyverse)

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_13species_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
#if ("gene_id" %in% colnames(ortholog_df)) {
#    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
#}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    dplyr::distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,"_togregaria.csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,"_togregaria.csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_I2_DEGs_Orthogroups_togregaria_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

STRATEGY 2: to own RefSeq

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to own RefSeq.

library(tidyverse)

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_13species_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)

# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,".csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,".csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_I2_DEGs_Orthogroups_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

Inflation I5

STRATEGY 1: to gregaria

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.

library(tidyverse)

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I5/Orthogroups_genesproteinbiotype_13species_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
#if ("gene_id" %in% colnames(ortholog_df)) {
#    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
#}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    dplyr::distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,"_togregaria.csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,"_togregaria.csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_I5_DEGs_Orthogroups_togregaria_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

STRATEGY 2: to own RefSeq

This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to own RefSeq.

library(tidyverse)

# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I5/Orthogroups_genesproteinbiotype_13species_annotated_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)

# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"

# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
    colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}

# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
    dplyr::select(GeneID, GeneType, Orthogroup, Description, Species) %>%
    distinct(GeneID, .keep_all = TRUE)

# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")

# Initialize an empty data frame for summary
summary_table <- data.frame()

# Loop through each species
for (species in species_list) {
    message(paste("Processing:", species))
    
    # Load DESeq2 results for Head and Thorax
    head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Head/DESeq2_sigresults_Head_", species,".csv"))
    thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq/", paste0(species, "/Thorax/DESeq2_sigresults_Thorax_", species,".csv"))
    
    # Check if files exist
    if (!file.exists(head_file) || !file.exists(thorax_file)) {
        message(paste("Missing DESeq2 results for:", species))
        next
    }
    
    head_data <- read.csv(head_file, stringsAsFactors = FALSE)
    thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
    
    # Ensure GeneID column exists
    if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
        colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
    }
    if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
        colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
    }
    
    # Convert GeneID to character
    head_data$GeneID <- as.character(head_data$GeneID)
    thorax_data$GeneID <- as.character(thorax_data$GeneID)
    ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
    
    # Merge with Orthogroups and ensure Orthogroup is always character
    head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))

    thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
        mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
    
    # Classify DEGs and add Tissue + Species columns
    head_merged <- head_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Head",   # Add Tissue column
            Species = species  # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included

    thorax_merged <- thorax_merged %>%
        mutate(
            Status = case_when(
                padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
                padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
                TRUE ~ "Not Significant"
            ),
            Tissue = "Thorax",  # Add Tissue column
            Species = species   # Add Species column (Fix!)
        ) %>%
        dplyr::select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status)  # Ensure Species column is included
    
    # Combine results
    summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}

# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
  pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")

# Create a searchable DataTable with color formatting
datatable(
  summary_table_pivot, 
  options = list(
    pageLength = 50,  # Show only the first 50 rows by default
    scrollX = TRUE,  # Enable horizontal scrolling if needed
    autoWidth = TRUE,  # Adjust column width automatically
    searchHighlight = TRUE  # Highlight search results
  ),
  rownames = FALSE,
  class = "compact"  # Applies a smaller font size
) %>%
  formatStyle(
    columns = names(summary_table_pivot)[-c(1,2)],  # Exclude Orthogroup and GeneID from color formatting
    backgroundColor = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("lightcoral", "lightblue")  # Red for Upregulated, Blue for Downregulated
    ),
    color = styleEqual(
      c("Upregulated", "Downregulated"), 
      c("white", "black")  # White text for Upregulated, Black text for Downregulated
    )
  )

# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_I5_DEGs_Orthogroups_May2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)

message(paste("Summary table saved at:", output_file))

Session information

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DT_0.33          kableExtra_1.4.0 lubridate_1.9.4  dplyr_1.1.4     
 [5] ggplot2_3.5.2    tidyverse_2.0.0  forcats_1.0.0    tibble_3.2.1    
 [9] purrr_1.0.4      stringr_1.5.1    readr_2.1.5      tidyr_1.3.1     

loaded via a namespace (and not attached):
 [1] sass_0.4.9         generics_0.1.3     xml2_1.3.7         stringi_1.8.4     
 [5] hms_1.1.3          digest_0.6.37      magrittr_2.0.3     evaluate_1.0.3    
 [9] grid_4.4.2         timechange_0.3.0   RColorBrewer_1.1-3 fastmap_1.2.0     
[13] rprojroot_2.0.4    workflowr_1.7.1    jsonlite_1.9.1     whisker_0.4.1     
[17] promises_1.3.2     crosstalk_1.2.1    viridisLite_0.4.2  scales_1.4.0      
[21] jquerylib_0.1.4    cli_3.6.5          crayon_1.5.3       rlang_1.1.6       
[25] bit64_4.6.0-1      withr_3.0.2        cachem_1.1.0       yaml_2.3.10       
[29] parallel_4.4.2     tools_4.4.2        tzdb_0.4.0         httpuv_1.6.15     
[33] vctrs_0.6.5        R6_2.6.1           lifecycle_1.0.4    git2r_0.35.0      
[37] bit_4.5.0.1        htmlwidgets_1.6.4  fs_1.6.5           vroom_1.6.5       
[41] pkgconfig_2.0.3    pillar_1.10.2      bslib_0.9.0        later_1.4.1       
[45] gtable_0.3.6       glue_1.8.0         Rcpp_1.0.14        systemfonts_1.2.1 
[49] xfun_0.51          tidyselect_1.2.1   rstudioapi_0.17.1  knitr_1.49        
[53] farver_2.1.2       htmltools_0.5.8.1  rmarkdown_2.29     svglite_2.1.3     
[57] compiler_4.4.2