Mercurial > repos > davidvanzessen > shm_csr

comparison pattern_plots.r @ 39:a24f8c93583a draft

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author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
parents 05c62efdc393
children 1cf60ae234b4
comparison
equal deleted inserted replaced
38:05c62efdc393 39:a24f8c93583a
54 54
55 data1 = data1[order(data1$Type),] 55 data1 = data1[order(data1$Type),]
56 56
57 write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T) 57 write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
58 58
59 p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL)) 59 p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL)) + ggtitle("Percentage of mutations in AID and pol eta motives")
60 p = p + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("RGYW.WRCY" = "white", "TW.WA" = "blue4")) 60 p = p + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("RGYW.WRCY" = "white", "TW.WA" = "blue4"))
61 #p = p + scale_colour_manual(values=c("RGYW.WRCY" = "black", "TW.WA" = "blue4")) 61 #p = p + scale_colour_manual(values=c("RGYW.WRCY" = "black", "TW.WA" = "blue4"))
62 png(filename=plot1.png, width=480, height=300) 62 png(filename=plot1.png, width=510, height=300)
63 print(p) 63 print(p)
64 dev.off() 64 dev.off()
65 65
66 data2 = dat[c(1, 5:8),] 66 data2 = dat[c(1, 5:8),]
67 67
91 91
92 data2 = data2[order(data2$Type),] 92 data2 = data2[order(data2$Type),]
93 93
94 write.table(data2, plot2.txt, quote=F, sep="\t", na="", row.names=F, col.names=T) 94 write.table(data2, plot2.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
95 95
96 p = ggplot(data2, aes(x=Class, y=value, fill=Type)) + geom_bar(position="fill", stat="identity", colour = "black") + scale_y_continuous(labels=percent_format()) + guides(fill=guide_legend(title=NULL)) + ylab("% of mutations") 96 p = ggplot(data2, aes(x=Class, y=value, fill=Type)) + geom_bar(position="fill", stat="identity", colour = "black") + scale_y_continuous(labels=percent_format()) + guides(fill=guide_legend(title=NULL)) + ylab("% of mutations") + ggtitle("Relative mutation patterns")
97 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white")) 97 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
98 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black")) 98 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black"))
99 png(filename=plot2.png, width=480, height=300) 99 png(filename=plot2.png, width=480, height=300)
100 print(p) 100 print(p)
101 dev.off() 101 dev.off()
120 data3["A/T",is.infinite(unlist(data3["A/T",]))] = 0 120 data3["A/T",is.infinite(unlist(data3["A/T",]))] = 0
121 121
122 data3 = melt(t(data3[8:10,])) 122 data3 = melt(t(data3[8:10,]))
123 names(data3) = c("Class", "Type", "value") 123 names(data3) = c("Class", "Type", "value")
124 124
125 chk = is.na(data1$data3) 125 chk = is.na(data3$value)
126 if(any(chk)){ 126 if(any(chk)){
127 data3[chk, "value"] = 0 127 data3[chk, "value"] = 0
128 } 128 }
129 129
130 data3 = data3[order(data3$Type),] 130 data3 = data3[order(data3$Type),]
131 131
132 write.table(data3, plot3.txt, quote=F, sep="\t", na="", row.names=F, col.names=T) 132 write.table(data3, plot3.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
133 133
134 p = ggplot(data3, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of nucleotides") + guides(fill=guide_legend(title=NULL)) 134 p = ggplot(data3, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of nucleotides") + guides(fill=guide_legend(title=NULL)) + ggtitle("Absolute mutation patterns")
135 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white")) 135 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
136 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black")) 136 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black"))
137 png(filename=plot3.png, width=480, height=300) 137 png(filename=plot3.png, width=480, height=300)
138 print(p) 138 print(p)
139 dev.off() 139 dev.off()