README.org

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-#+title: Comparative Genomics Project
-#+author: Samuel Ortion
-#+date: 2024-2025
-
-Analysis of Tandemly Arrayed Genes in /Glycine max/ (soy) proteome.
-
-Part of the "Comparative Genomics" teaching unit in M2 GENomics Informatics and Mathematics for Health and Environment (GENIOMHE) at Université d'Évry Paris-Saclay.

environment.yml

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- 

renv/.gitignore

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-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/

renv/settings.json

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-{
-  "bioconductor.version": null,
-  "external.libraries": [],
-  "ignored.packages": [],
-  "package.dependency.fields": [
-    "Imports",
-    "Depends",
-    "LinkingTo"
-  ],
-  "ppm.enabled": null,
-  "ppm.ignored.urls": [],
-  "r.version": null,
-  "snapshot.type": "implicit",
-  "use.cache": true,
-  "vcs.ignore.cellar": true,
-  "vcs.ignore.library": true,
-  "vcs.ignore.local": true,
-  "vcs.manage.ignores": true
-}

src/family_size_hist.R

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-#!/usr/bin/env Rscript
-library(dplyr)
-library(ggplot2)
-
-args <- commandArgs(trailingOnly=TRUE)
-input_file <- args[1]
-output_file <- args[2]
-title <- args[3]
-
-family_df <- read.table(input_file, header=FALSE)
-colnames(family_df) <- c("geneid", "familyid")
-
-count_df <- family_df %>% count(familyid)
-distribution_df <- count_df %>% count(n)
-
-theme_set(theme_grey(base_size=20))
-
-ggplot(distribution_df, aes(x=n, y=nn)) +
-  geom_bar(stat='identity') +
-  labs(title="Duplicate Gene Family Sizes",
-       subtitle=title) +
-  xlab("family size") +
-  ylab("count")
-ggsave(output_file)