Mercurial > repos > davidvanzessen > shm_csr
diff shm_csr.r @ 39:a24f8c93583a draft
Uploaded
author | davidvanzessen |
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date | Thu, 22 Dec 2016 09:39:27 -0500 |
parents | 8d1c4c75f81b |
children | 1cf60ae234b4 |
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--- a/shm_csr.r Tue Dec 20 09:03:15 2016 -0500 +++ b/shm_csr.r Thu Dec 22 09:39:27 2016 -0500 @@ -302,14 +302,14 @@ 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("") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) + p = p + xlab("From base") + ylab("") + ggtitle("Bargraph transition information") + 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(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")) + p = p + xlab("To base") + ylab("From Base") + ggtitle("Heatmap transition information") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black")) print(p) dev.off() } else { @@ -388,7 +388,7 @@ pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGA1" = "lightblue1", "IGA2" = "blue4")) pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"), axis.title=element_blank(), axis.text=element_blank(), axis.ticks=element_blank()) - pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclasses", "( n =", sum(genesForPlot$Freq), ")")) + pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclass distribution", "( n =", sum(genesForPlot$Freq), ")")) write.table(genesForPlot, "IGA_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) png(filename="IGA.png") @@ -409,7 +409,7 @@ pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred")) pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"), axis.title=element_blank(), axis.text=element_blank(), axis.ticks=element_blank()) - pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclasses", "( n =", sum(genesForPlot$Freq), ")")) + pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclass distribution", "( n =", sum(genesForPlot$Freq), ")")) write.table(genesForPlot, "IGG_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) png(filename="IGG.png") @@ -430,7 +430,7 @@ p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black")) p = p + scale_fill_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) -p = p + scale_colour_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) +p = p + scale_colour_manual(guide = guide_legend(title = "Subclass"), values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) png(filename="scatter.png") print(p) @@ -454,7 +454,7 @@ p = ggplot(frequency_bins_data, aes(frequency_bins, frequency)) p = p + geom_bar(aes(fill=best_match_class), stat="identity", position="dodge") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black")) -p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) +p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(guide = guide_legend(title = "Class"), values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) png(filename="frequency_ranges.png") print(p)