Mercurial > repos > davidvanzessen > shm_csr
changeset 24:9955b23db68c draft
Uploaded
author | davidvanzessen |
---|---|
date | Fri, 02 Dec 2016 05:51:13 -0500 |
parents | 81453585dfc3 |
children | 8d1c4c75f81b |
files | shm_csr.r |
diffstat | 1 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/shm_csr.r Thu Dec 01 09:32:06 2016 -0500 +++ b/shm_csr.r Fri Dec 02 05:51:13 2016 -0500 @@ -177,7 +177,8 @@ write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T) -base.order = data.frame(base=c("A", "T", "C", "G"), order=1:4) +base.order.x = data.frame(base=c("A", "C", "G", "T"), order.x=1:4) +base.order.y = data.frame(base=c("T", "G", "C", "A"), order.y=1:4) calculate_result = function(i, gene, dat, matrx, f, fname, name){ tmp = dat[grepl(paste("^", gene, ".*", sep=""), dat$best_match),] @@ -291,24 +292,24 @@ transition2 = melt(transition, id.vars="id") - transition2 = merge(transition2, base.order, by.x="id", by.y="base") + transition2 = merge(transition2, base.order.x, by.x="id", by.y="base") - transition2 = merge(transition2, base.order, by.x="variable", by.y="base") + transition2 = merge(transition2, base.order.y, by.x="variable", by.y="base") transition2[is.na(transition2$value),]$value = 0 - if(any(transition2$value != 0)){ #having rows of data but a transition table filled with 0 is bad + if(any(transition2$value != 0)){ #having a transition table filled with 0 is bad print("Plotting heatmap and transition") png(filename=paste("transitions_stacked_", name, ".png", sep="")) p = ggplot(transition2, aes(factor(reorder(id, order.x)), y=value, fill=factor(reorder(variable, order.y)))) + geom_bar(position="fill", stat="identity", colour="black") #stacked bar - p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) + p = p + xlab("From base") + ylab("") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black")) + scale_fill_manual(values=c("A" = "blue4", "G" = "lightblue1", "C" = "olivedrab3", "T" = "olivedrab4")) #p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black")) print(p) dev.off() png(filename=paste("transitions_heatmap_", name, ".png", sep="")) - p = ggplot(transition2, aes(factor(reorder(id, order.x)), factor(reorder(variable, order.y)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap - p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) + p = ggplot(transition2, aes(factor(reorder(variable, -order.y)), factor(reorder(id, -order.x)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap + p = p + xlab("To base") + ylab("From Base") + ggtitle("Mutations frequency from base to base") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) print(p) dev.off() } else {