diff R/micropan_rarefaction.R @ 3:e42d30da7a74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/R/micropan_rarefaction.R	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,76 @@
+#!/usr/bin/R
+
+
+library(micropan)
+library(dendextend)
+library("optparse")
+
+
+option_list = list(
+  make_option(c("-f", "--file"), type="character", default=NULL,
+              help="dataset file name", metavar="character"),
+  make_option(c("-o", "--out"), type="character", default="out.txt",
+              help="output file name [default= %default]", metavar="character"),
+  make_option(c("-a", "--alpha"), type="character", default="heaps.tsv",
+              help="Heaps output file name [default= %default]", metavar="character"),
+  make_option(c("-p", "--pdf"), type="character", default="out.pdf",
+              help="PDF output file name [default= %default]", metavar="character")
+);
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if (is.null(opt$file)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (input file).\n", call.=FALSE)
+}
+
+if (is.null(opt$out)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (out file).\n", call.=FALSE)
+}
+if (is.null(opt$alpha)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (out file).\n", call.=FALSE)
+}
+if (is.null(opt$pdf)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (out file).\n", call.=FALSE)
+}
+
+
+# Loading a pan-matrix in this package 
+#data(xmpl.panmat)
+
+mydata <- read.table(opt$file, header=TRUE,sep="\t", row.names="Gene")
+tmydata<-t(mydata)
+#xmpl.panmat
+
+rarefaction = rarefaction(tmydata, n.perm = 100)
+write.table(
+  rarefaction,
+  opt$out,
+  row.names = FALSE,
+  quote = FALSE,
+  sep = '\t')
+
+
+# Estimating population openness
+h.est <- heaps(tmydata, n.perm = 100)
+write.table(
+  h.est,
+  opt$alpha,
+  row.names = TRUE,
+  quote = FALSE,
+  sep = '\t')
+
+# If alpha < 1 it indicates an open pan-genome
+
+pdf(opt$pdf)
+
+library(ggplot2)
+library(tidyr)
+rarefaction %>%
+gather(key = "Permutation", value = "Clusters", -Genome) %>%
+ggplot(aes(x = Genome, y = Clusters, group = Permutation)) +
+geom_point() +
+stat_summary(aes(y = Clusters,group=1), fun=mean, colour="red", geom="line",group=1)