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figureNoFilter.R
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137 lines (123 loc) · 5.92 KB
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#George Marchment + Clemence Sebe
#R script pour faire des distributions
#!/usr/bin/env Rscript
library(lattice)
#Script creating the graphs for the NoneFilterd SNP
#Retrieving Arguments given by the python script
args = commandArgs(trailingOnly=TRUE)
entree= args[1]
sortie = args[2]
#Reading the File
annot.file = entree
annotations = read.table(annot.file, h=TRUE,na.strings=".")
##Graph ("courbe.pdf")
pdf(paste(sortie, "courbe.pdf", sep = "", collapse=NULL))
plot(density(annotations$QD,na.rm=T),main="QD", sub = " QD " )
plot(density(annotations$FS,na.rm=T),main="FS", sub = " FS " )
plot(density(annotations$MQ,na.rm=T),main="MQ", sub = " MQ " )
plot(density(annotations$MQRankSum,na.rm=T),main="MQRankSum", sub = " MQRankSum " )
plot(density(annotations$ReadPosRankSum,na.rm=T),main="ReadPosRankSum", sub = " ReadPosRankSum " )
plot(density(annotations$SOR,na.rm=T),main="SOR", sub = " SOR " )
##Histogram
pdf(paste(sortie,"histogramme.pdf", sep = "", collapse=NULL))
hist(annotations$QD, breaks = 20, main= "QD", col = "steelblue")
hist(annotations$FS, breaks = 20, main= "FS", col = "steelblue")
hist(annotations$MQ, breaks = 20, main= "MQ", col = "steelblue")
hist(annotations$MQRankSum, breaks = 20, main= "MQRankSum", col = "steelblue")
hist(annotations$ReadPosRankSum, breaks = 20,main= "ReadPosRankSum", col = "steelblue")
hist(annotations$SOR, breaks = 20, main= "SOR", col = "steelblue")
##Standard deviation "Box"
pdf(paste(sortie,"repartition.pdf", sep = "", collapse=NULL))
boxplot(annotations$QD, range=0, main= "QD", horizontal=TRUE)
boxplot(annotations$FS, range=0, main= "FS", horizontal=TRUE)
boxplot(annotations$MQ, range=0, main= "MQ", horizontal=TRUE)
boxplot(annotations$MQRankSum, range=0, main= "MQRankSum", horizontal=TRUE)
boxplot(annotations$ReadPosRankSum, range=0, main= "ReadPosRankSum", horizontal=TRUE)
boxplot(annotations$SOR, range=0, main= "SOR", horizontal=TRUE)
#Reste of the Data written
fichier <- file(paste(sortie,"autreInfo.txt", sep = "", collapse=NULL), open="w")
val <- "QD :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$QD,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$QD,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$QD,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$QD,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$QD,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
val <- "FS :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$FS,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$FS,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$FS,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$FS,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$FS,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
val <- "MQ :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$MQ,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$MQ,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$MQ,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$MQ,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$MQ,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
val <- "MQRankSum :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$MQRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$MQRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$MQRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$MQRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$MQRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
val <- "ReadPosRankSum :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$ReadPosRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$ReadPosRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$ReadPosRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$ReadPosRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$ReadPosRankSum,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
val <- "SOR :"
writeLines(val, con = fichier)
val <- paste("Moyenne : ", mean(annotations$SOR,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Mediane : ", median(annotations$SOR,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Maximum : ", max(annotations$SOR,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Minimum : ", min(annotations$SOR,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- paste("Ecart-type : ", sd(annotations$SOR,na.rm=T), sep ="", collapse=NULL)
writeLines(val, con = fichier)
val <- " "
writeLines(val, con = fichier)
close(fichier)