Mercurial > repos > davidvanzessen > shm_csr
comparison pattern_plots.r @ 38:05c62efdc393 draft
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author | davidvanzessen |
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date | Tue, 20 Dec 2016 09:03:15 -0500 |
parents | 81453585dfc3 |
children | a24f8c93583a |
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37:767dd9327009 | 38:05c62efdc393 |
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45 | 45 |
46 data1 = melt(t(data1)) | 46 data1 = melt(t(data1)) |
47 | 47 |
48 names(data1) = c("Class", "Type", "value") | 48 names(data1) = c("Class", "Type", "value") |
49 | 49 |
50 chk = is.na(data1$value) | |
51 if(any(chk)){ | |
52 data1[chk, "value"] = 0 | |
53 } | |
54 | |
50 data1 = data1[order(data1$Type),] | 55 data1 = data1[order(data1$Type),] |
51 | 56 |
52 write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T) | 57 write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T) |
53 | 58 |
54 p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL)) | 59 p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL)) |
77 | 82 |
78 data2 = melt(t(data2[c("A/T","G/C transitions","G/C transversions"),])) | 83 data2 = melt(t(data2[c("A/T","G/C transitions","G/C transversions"),])) |
79 | 84 |
80 names(data2) = c("Class", "Type", "value") | 85 names(data2) = c("Class", "Type", "value") |
81 | 86 |
87 chk = is.na(data2$value) | |
88 if(any(chk)){ | |
89 data2[chk, "value"] = 0 | |
90 } | |
91 | |
82 data2 = data2[order(data2$Type),] | 92 data2 = data2[order(data2$Type),] |
83 | 93 |
84 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) |
85 | 95 |
86 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") |
91 dev.off() | 101 dev.off() |
92 | 102 |
93 data3 = dat[c(5, 6, 8, 17:20),] | 103 data3 = dat[c(5, 6, 8, 17:20),] |
94 data3 = data3[,names(data3)[grepl("\\.x", names(data3))]] | 104 data3 = data3[,names(data3)[grepl("\\.x", names(data3))]] |
95 names(data3) = gsub(".x", "", names(data3)) | 105 names(data3) = gsub(".x", "", names(data3)) |
96 | |
97 data3[is.na(data3)] = 0 | |
98 #data3[is.infinite(data3)] = 0 | |
99 | 106 |
100 data3["G/C transitions",] = round(data3["Transitions at G C (%)",] / (data3["C",] + data3["G",]) * 100, 1) | 107 data3["G/C transitions",] = round(data3["Transitions at G C (%)",] / (data3["C",] + data3["G",]) * 100, 1) |
101 | 108 |
102 data3["G/C transversions",] = round((data3["Targeting of G C (%)",] - data3["Transitions at G C (%)",]) / (data3["C",] + data3["G",]) * 100, 1) | 109 data3["G/C transversions",] = round((data3["Targeting of G C (%)",] - data3["Transitions at G C (%)",]) / (data3["C",] + data3["G",]) * 100, 1) |
103 | 110 |
112 data3["A/T",is.nan(unlist(data3["A/T",]))] = 0 | 119 data3["A/T",is.nan(unlist(data3["A/T",]))] = 0 |
113 data3["A/T",is.infinite(unlist(data3["A/T",]))] = 0 | 120 data3["A/T",is.infinite(unlist(data3["A/T",]))] = 0 |
114 | 121 |
115 data3 = melt(t(data3[8:10,])) | 122 data3 = melt(t(data3[8:10,])) |
116 names(data3) = c("Class", "Type", "value") | 123 names(data3) = c("Class", "Type", "value") |
124 | |
125 chk = is.na(data1$data3) | |
126 if(any(chk)){ | |
127 data3[chk, "value"] = 0 | |
128 } | |
117 | 129 |
118 data3 = data3[order(data3$Type),] | 130 data3 = data3[order(data3$Type),] |
119 | 131 |
120 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) |
121 | 133 |