Extra figures
Ha Tran
2024-01-12
Last updated: 2024-01-13
Checks: 7 0
Knit directory: 4_Treg_uNK/1_analysis/
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Untracked: 2_plots/functionalHeat_DT vs PBS.svg
Untracked: 2_plots/functionalHeat_Treg vs DT.svg
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Unstaged changes:
Modified: 0_data/rds_objects/comp.rds
Modified: 0_data/rds_objects/dge.rds
Modified: 0_data/rds_objects/enrichGO.rds
Modified: 0_data/rds_objects/enrichGO_sig.rds
Modified: 0_data/rds_objects/enrichKEGG.rds
Modified: 0_data/rds_objects/enrichKEGG_all.rds
Modified: 0_data/rds_objects/enrichKEGG_sig.rds
Modified: 0_data/rds_objects/lm.rds
Modified: 0_data/rds_objects/lm_all.rds
Modified: 0_data/rds_objects/lm_sig.rds
Modified: 1_analysis/_site.yml
Deleted: 1_analysis/gsea.Rmd
Modified: 2_plots/1_QC/counts_after_filtering.svg
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Modified: 2_plots/1_QC/counts_before_filtering.svg
Modified: 2_plots/1_QC/library_size.svg
Modified: 2_plots/2_DE/heat_DT vs PBS.svg
Modified: 2_plots/2_DE/heat_Treg vs DT.svg
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Modified: 2_plots/2_DE/hist_DT vs PBS.svg
Modified: 2_plots/2_DE/hist_Treg vs DT.svg
Modified: 2_plots/2_DE/hist_Treg vs PBS.svg
Modified: 2_plots/2_DE/ma_DT vs PBS.png
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Modified: 2_plots/2_DE/venn.png
Modified: 2_plots/2_DE/vol_DT vs PBS.png
Modified: 2_plots/2_DE/vol_Treg vs DT.png
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Modified: 2_plots/3_FA/kegg/venn.png
Modified: 2_plots/sampleHeat.svg
Modified: 3_output/GO_sig.xlsx
Modified: 3_output/KEGG_all.xlsx
Modified: 3_output/KEGG_sig.xlsx
Modified: 3_output/de_genes_all.xlsx
Modified: 3_output/de_genes_sig.xlsx
Modified: 3_output/reactome_all.xlsx
Modified: 3_output/reactome_sig.xlsx
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a957cff | Ha Manh Tran | 2024-01-13 | workflowr::wflow_publish(here::here("1_analysis/*Rmd")) |
| Rmd | c78dfac | tranmanhha135 | 2024-01-12 | remote from ipad |
# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(DT)
library(extrafont)
library(VennDiagram)
# Custom ggplot
library(gridExtra)
library(ggbiplot)
library(ggrepel)
library(rrvgo)
library(d3treeR)
library(plotly)
library(GOSemSim)
library(data.table)
# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(patchwork)
library(pandoc)
library(knitr)
opts_knit$set(progress = FALSE, verbose = FALSE)
opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)Extra Figures
[1] "Gzmb" "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg" "Lamp1" "Prf1" "Srgn"
[1] "B2m" "Ctsc" "Gzmb" "H2-D1" "H2-K1" "H2-Q4"
[7] "H2-T23" "Prf1" "Ptprc" "Serpinb9" "Tap2"
[1] "Gzmb" "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg" "Prf1"
[1] "Gzmb" "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg"
[7] "Havcr2" "Lamp1" "Serpinb9" "Tap1" "Tap2"
[1] "B2m" "H2-D1" "H2-K1" "H2-Q4" "H2-T23" "Havcr2"
[7] "Lamp1" "Ptprc" "Serpinb9" "Tap1" "Tap2"
[1] "H2-D1" "H2-K1" "H2-Q4" "H2-T23"
[1] "B2m" "H2-D1" "H2-K1" "H2-Q4" "H2-T23" "Hspa1b" "Psme1" "Psme2"
[9] "Tap1" "Tap2"
[1] "Adam8" "Cdh1" "Col4a5" "Col4a6" "Col7a1" "Ctsg" "Ctsk" "Mmp14"
[9] "Mmp15" [1] "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg" "Lamp1"
[1] "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg"
[1] "Gzmc" "Gzmd" "Gzme" "Gzmf" "Gzmg" "Lamp1"
[1] "B2m" "H2-D1" "H2-K1" "H2-T23"
[1] "B2m" "H2-D1" "H2-K1" "H2-T23" "Lamp1"
[1] "H2-D1" "H2-K1" "H2-T23"
[1] "B2m" "H2-D1" "H2-K1" "H2-T23" "Hspa1l" "Rfxap"
[1] "Adam8" "Adamts4" "Eln" "Spp1" png
2 
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
time zone: Australia/Adelaide
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggplotify_0.1.2 RColorBrewer_1.1-3 ComplexHeatmap_2.16.0
[4] knitr_1.45 pandoc_0.2.0 patchwork_1.1.3
[7] enrichplot_1.20.3 org.Mm.eg.db_3.17.0 AnnotationDbi_1.62.2
[10] IRanges_2.34.1 S4Vectors_0.38.2 Biobase_2.60.0
[13] BiocGenerics_0.46.0 clusterProfiler_4.8.3 Glimma_2.10.0
[16] edgeR_3.42.4 limma_3.56.2 data.table_1.14.10
[19] GOSemSim_2.26.1 plotly_4.10.3 d3treeR_0.1
[22] rrvgo_1.12.2 ggrepel_0.9.4 ggbiplot_0.55
[25] scales_1.3.0 plyr_1.8.9 gridExtra_2.3
[28] VennDiagram_1.7.3 futile.logger_1.4.3 extrafont_0.19
[31] DT_0.31 kableExtra_1.3.4 lubridate_1.9.3
[34] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2
[37] tidyr_1.3.0 ggplot2_3.4.4 tidyverse_2.0.0
[40] reshape2_1.4.4 tibble_3.2.1 readr_2.1.4
[43] magrittr_2.0.3 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] fs_1.6.3 matrixStats_1.2.0
[3] bitops_1.0-7 HDO.db_0.99.1
[5] httr_1.4.7 webshot_0.5.5
[7] doParallel_1.0.17 tools_4.3.1
[9] utf8_1.2.4 R6_2.5.1
[11] lazyeval_0.2.2 GetoptLong_1.0.5
[13] withr_2.5.2 cli_3.6.1
[15] formatR_1.14 scatterpie_0.2.1
[17] labeling_0.4.3 slam_0.1-50
[19] sass_0.4.8 tm_0.7-11
[21] askpass_1.2.0 systemfonts_1.0.5
[23] yulab.utils_0.1.1 gson_0.1.0
[25] DOSE_3.26.2 svglite_2.1.3
[27] rstudioapi_0.15.0 RSQLite_2.3.4
[29] treemap_2.4-4 generics_0.1.3
[31] gridGraphics_0.5-1 shape_1.4.6
[33] GO.db_3.17.0 Matrix_1.6-4
[35] fansi_1.0.6 abind_1.4-5
[37] lifecycle_1.0.4 whisker_0.4.1
[39] yaml_2.3.7 SummarizedExperiment_1.30.2
[41] qvalue_2.32.0 blob_1.2.4
[43] promises_1.2.1 crayon_1.5.2
[45] lattice_0.21-8 cowplot_1.1.2
[47] KEGGREST_1.40.1 magick_2.8.2
[49] pillar_1.9.0 fgsea_1.26.0
[51] GenomicRanges_1.52.1 rjson_0.2.21
[53] codetools_0.2-19 fastmatch_1.1-4
[55] glue_1.6.2 downloader_0.4
[57] ggfun_0.1.3 vctrs_0.6.5
[59] png_0.1-8 treeio_1.24.3
[61] gtable_0.3.4 cachem_1.0.8
[63] xfun_0.39 S4Arrays_1.0.6
[65] mime_0.12 tidygraph_1.3.0
[67] pheatmap_1.0.12 iterators_1.0.14
[69] ellipsis_0.3.2 nlme_3.1-164
[71] ggtree_3.8.2 bit64_4.0.5
[73] GenomeInfoDb_1.36.4 rprojroot_2.0.4
[75] data.tree_1.1.0 bslib_0.6.1
[77] colorspace_2.1-0 DBI_1.2.0
[79] DESeq2_1.40.2 tidyselect_1.2.0
[81] bit_4.0.5 compiler_4.3.1
[83] extrafontdb_1.0 git2r_0.33.0
[85] rvest_1.0.3 xml2_1.3.6
[87] NLP_0.2-1 DelayedArray_0.26.7
[89] shadowtext_0.1.2 rappdirs_0.3.3
[91] digest_0.6.33 rmarkdown_2.25
[93] XVector_0.40.0 htmltools_0.5.7
[95] pkgconfig_2.0.3 umap_0.2.10.0
[97] MatrixGenerics_1.12.3 highr_0.10
[99] fastmap_1.1.1 rlang_1.1.1
[101] GlobalOptions_0.1.2 htmlwidgets_1.6.4
[103] shiny_1.8.0 farver_2.1.1
[105] jquerylib_0.1.4 jsonlite_1.8.8
[107] BiocParallel_1.34.2 RCurl_1.98-1.13
[109] GenomeInfoDbData_1.2.10 wordcloud_2.6
[111] munsell_0.5.0 Rcpp_1.0.11
[113] ape_5.7-1 viridis_0.6.4
[115] reticulate_1.34.0 stringi_1.8.3
[117] ggraph_2.1.0 zlibbioc_1.46.0
[119] MASS_7.3-60 parallel_4.3.1
[121] Biostrings_2.68.1 graphlayouts_1.0.2
[123] splines_4.3.1 hms_1.1.3
[125] circlize_0.4.15 locfit_1.5-9.8
[127] igraph_1.6.0 futile.options_1.0.1
[129] XML_3.99-0.16 evaluate_0.23
[131] lambda.r_1.2.4 tzdb_0.4.0
[133] foreach_1.5.2 tweenr_2.0.2
[135] httpuv_1.6.13 Rttf2pt1_1.3.12
[137] openssl_2.1.1 polyclip_1.10-6
[139] clue_0.3-65 gridBase_0.4-7
[141] ggforce_0.4.1 xtable_1.8-4
[143] RSpectra_0.16-1 tidytree_0.4.6
[145] later_1.3.2 viridisLite_0.4.2
[147] aplot_0.2.2 memoise_2.0.1
[149] cluster_2.1.4 workflowr_1.7.1
[151] timechange_0.2.0 here_1.0.1
[153] gridSVG_1.7-5