diff --git a/.gitignore b/.gitignore index f0fed7e..3ca1610 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ .DS_Store */.DS_Store +result/* diff --git a/Rscript/Distance_counting.r b/Rscript/Distance_counting.r index afafb9a..91aadc1 100644 --- a/Rscript/Distance_counting.r +++ b/Rscript/Distance_counting.r @@ -86,7 +86,7 @@ distance = c(rep("0-0.5kbp" , 2), rep("0.5-1kbp" , 2), rep("1-2kbp", 2), rep("2k strand = rep(c("+","-"),4) value_down = c(c1[2],c9[2],c2[2],c10[2],c3[2],c11[2],c4[2],c12[2]) data = data.frame(distance,strand,value_down) -plot2 = ggplot(data, aes(fill=strand, y=value_down, x=distance )) + geom_bar(position="dodge", stat="identity") + ggtitle("Mandshurica") + ylab("number of LTR") + xlab("distance to the gene") + theme(plot.title = element_text(hjust = 0.5)) +plot2 = ggplot(data, aes(fill=strand, y=value_down, x=distance )) + geom_bar(position="dodge", stat="identity") + ggtitle("Number of LTR with an adjacent downstream gene") + ylab("number of LTR") + xlab("distance to the gene") + theme(plot.title = element_text(hjust = 0.5)) print(plot2) invisible(dev.off()) print("Plots generated") diff --git a/Rscript/Overlap_counting.r b/Rscript/Overlap_counting.r index e72cc3f..b8e2710 100644 --- a/Rscript/Overlap_counting.r +++ b/Rscript/Overlap_counting.r @@ -93,7 +93,7 @@ strand = rep(c("+","-"),2) value = c(c1[1],c2[1],c1[2],c2[2]) data = data.frame(sens,value) pdf(opt$pdf) -plot = ggplot(data, aes(fill=strand, y=value, x=sens )) + geom_bar(position="dodge", stat="identity") + ggtitle("Sibirica") + ylab("number of TE with an overlapping gene") + xlab("") + theme(plot.title = element_text(hjust = 0.5)) +plot = ggplot(data, aes(fill=strand, y=value, x=sens )) + geom_bar(position="dodge", stat="identity") + ggtitle("Dataset") + ylab("Number of TE with an overlapping gene") + xlab("") + theme(plot.title = element_text(hjust = 0.5)) print(plot) invisible(dev.off()) print("INFO - Plot created")