Last updated: 2025-06-05

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Knit directory: locust-comparative-genomics/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    code/.DS_Store
    Ignored:    code/scripts/.DS_Store
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    Ignored:    data/DEG_results/Bulk_RNAseq/cancellata/Thorax/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/cubense/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/davidO/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/gregaria/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/nitens/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/piceifrons/.DS_Store
    Ignored:    data/DEG_results/RNAi/.DS_Store
    Ignored:    data/DEG_results/RNAi/All/.DS_Store
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    Ignored:    data/DEG_results/RNAi/Head/.DS_Store
    Ignored:    data/DEG_results/RNAi/Head_control/.DS_Store
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    Ignored:    data/DEG_results/RNAi/Thorax_no_rRNA/.DS_Store
    Ignored:    data/DEG_results/gregaria/
    Ignored:    data/DEG_results/single_cell/.DS_Store
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Untracked files:
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Unstaged changes:
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    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
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    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_cubense.png
    Modified:   data/overlap/Bulk_RNAseq/scatter_plot_overlapping_genes_piceifrons.png

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/2_hic-snps-phylogeny.Rmd) and HTML (docs/2_hic-snps-phylogeny.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
html 3e696d6 Maeva TECHER 2025-06-05 Adding ortho heatmap
html 285370e Maeva TECHER 2025-06-04 Build site.
Rmd cacc1db Maeva TECHER 2025-05-02 updates files

Ask Sheina to add her scripts

So we have merged the snps.

module purge ml GCC/12.3.0 vcflib/1.0.9-R-4.3.2 BCFtools/1.18

we will subsample the number of snps so we can run the stats on it

bcftools view all_samples.vcf.gz | vcfrandomsample -r 0.02 > all_samples_subset.vcf

module purge ml GCC/13.2.0 OpenMPI/4.1.6 R_tamu/4.4.1 export R_LIBS=$SCRATCH/R_LIBS_USER/

library(tidyverse) library(ggplot2)

Load and parse data

var_depth <- read_delim(“all_samples.ldepth.mean”, delim = “, col_names = c(”chr”, “pos”, “mean_depth”, “var_depth”), skip = 1)

Compute the mean

summary(var_depth\(mean_depth) mean_val <- mean(var_depth\)mean_depth, na.rm = TRUE)

Base plot with vertical mean line

a <- ggplot(var_depth, aes(mean_depth)) + geom_density(fill = “dodgerblue1”, colour = “black”, alpha = 0.3) + geom_vline(xintercept = mean_val, colour = “red”, linetype = “dashed”) + theme_light()

Open a multi-page PDF

pdf(“mean_depth_density.pdf”, width = 6, height = 4)

Page 1: full density plot

print(a)

Page 2: zoomed in

a_zoom <- a + xlim(0, 100) print(a_zoom)

Close device

dev.off()

Load missingness data

var_miss <- read_delim(“all_samples.lmiss”, delim = “, col_names = c(”chr”, “pos”, “nchr”, “nfiltered”, “nmiss”, “fmiss”), skip = 1)

Calculate mean missingness

summary(var_miss\(fmiss) mean_fmiss <- mean(var_miss\)fmiss, na.rm = TRUE)

Base plot with vertical mean line

a <- ggplot(var_miss, aes(fmiss)) + geom_density(fill = “dodgerblue1”, colour = “black”, alpha = 0.3) + geom_vline(xintercept = mean_fmiss, colour = “red”, linetype = “dashed”) + theme_light()

Open multi-page PDF

pdf(“variant_missingness.pdf”, width = 6, height = 4)

Page 1: full density plot

print(a)

Page 2: zoomed in

a_zoom <- a + xlim(0, 1) # fmiss is a fraction (0–1), not 0–100 print(a_zoom)

Close device

dev.off()

Load individual depth data

ind_depth <- read_delim(“all_samples.idepth”, delim = “, col_names = c(”ind”, “nsites”, “depth”), skip = 1)

Calculate mean depth per individual

mean_depth <- mean(ind_depth$depth, na.rm = TRUE)

Create histogram with vertical mean line

a <- ggplot(ind_depth, aes(depth)) + geom_histogram(fill = “dodgerblue1”, colour = “black”, alpha = 0.3, bins = 30) + geom_vline(xintercept = mean_depth, colour = “red”, linetype = “dashed”) + theme_light()

Open PDF for two pages

pdf(“individual_depth_distribution.pdf”, width = 6, height = 4)

Page 1: full view

print(a)

Page 2: zoomed in (e.g., 0 to 100)

a_zoom <- a + xlim(0, 100) print(a_zoom)

Close the PDF device

dev.off()

Load individual missingness data

ind_miss <- read_delim(“all_samples.imiss”, delim = “, col_names = c(”ind”, “ndata”, “nfiltered”, “nmiss”, “fmiss”), skip = 1)

Calculate mean missingness

mean_fmiss <- mean(ind_miss$fmiss, na.rm = TRUE)

Create histogram with vertical line

a <- ggplot(ind_miss, aes(fmiss)) + geom_histogram(fill = “dodgerblue1”, colour = “black”, alpha = 0.3, bins = 30) + geom_vline(xintercept = mean_fmiss, colour = “red”, linetype = “dashed”) + theme_light()

Save to multi-page PDF

pdf(“individual_missingness_distribution.pdf”, width = 6, height = 4)

Page 1: full histogram

print(a)

Page 2: zoomed-in view

a_zoom <- a + xlim(0, 1) print(a_zoom)

Close PDF device

dev.off()


sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5

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] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.5         knitr_1.49       
 [5] rlang_1.1.6       xfun_0.51         stringi_1.8.4     processx_3.8.6   
 [9] promises_1.3.2    jsonlite_1.9.1    glue_1.8.0        rprojroot_2.0.4  
[13] git2r_0.35.0      htmltools_0.5.8.1 httpuv_1.6.15     ps_1.9.0         
[17] sass_0.4.9        rmarkdown_2.29    jquerylib_0.1.4   tibble_3.2.1     
[21] evaluate_1.0.3    fastmap_1.2.0     yaml_2.3.10       lifecycle_1.0.4  
[25] whisker_0.4.1     stringr_1.5.1     compiler_4.4.2    fs_1.6.5         
[29] pkgconfig_2.0.3   Rcpp_1.0.14       rstudioapi_0.17.1 later_1.4.1      
[33] digest_0.6.37     R6_2.6.1          pillar_1.10.2     callr_3.7.6      
[37] magrittr_2.0.3    bslib_0.9.0       tools_4.4.2       cachem_1.1.0     
[41] getPass_0.2-4