Mercurial > repos > davidvanzessen > shm_csr

comparison pattern_plots.r @ 42:1cf60ae234b4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Tue, 28 Mar 2017 08:25:36 -0400
parents a24f8c93583a
children
comparison
equal deleted inserted replaced
41:b8ac74723ab0 42:1cf60ae234b4
7 input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt" 7 input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt"
8 8
9 plot1.path = args[2] 9 plot1.path = args[2]
10 plot1.png = paste(plot1.path, ".png", sep="") 10 plot1.png = paste(plot1.path, ".png", sep="")
11 plot1.txt = paste(plot1.path, ".txt", sep="") 11 plot1.txt = paste(plot1.path, ".txt", sep="")
12 plot1.pdf = paste(plot1.path, ".pdf", sep="")
12 13
13 plot2.path = args[3] 14 plot2.path = args[3]
14 plot2.png = paste(plot2.path, ".png", sep="") 15 plot2.png = paste(plot2.path, ".png", sep="")
15 plot2.txt = paste(plot2.path, ".txt", sep="") 16 plot2.txt = paste(plot2.path, ".txt", sep="")
17 plot2.pdf = paste(plot2.path, ".pdf", sep="")
16 18
17 plot3.path = args[4] 19 plot3.path = args[4]
18 plot3.png = paste(plot3.path, ".png", sep="") 20 plot3.png = paste(plot3.path, ".png", sep="")
19 plot3.txt = paste(plot3.path, ".txt", sep="") 21 plot3.txt = paste(plot3.path, ".txt", sep="")
22 plot3.pdf = paste(plot3.path, ".pdf", sep="")
20 23
21 clean.output = args[5] 24 clean.output = args[5]
22 25
23 dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T, row.names=1) 26 dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T, row.names=1)
24
25
26 27
27 classes = c("IGA", "IGA1", "IGA2", "IGG", "IGG1", "IGG2", "IGG3", "IGG4", "IGM", "IGE") 28 classes = c("IGA", "IGA1", "IGA2", "IGG", "IGG1", "IGG2", "IGG3", "IGG4", "IGM", "IGE")
28 xyz = c("x", "y", "z") 29 xyz = c("x", "y", "z")
29 new.names = c(paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep=".")) 30 new.names = c(paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))
30 31
61 #p = p + scale_colour_manual(values=c("RGYW.WRCY" = "black", "TW.WA" = "blue4")) 62 #p = p + scale_colour_manual(values=c("RGYW.WRCY" = "black", "TW.WA" = "blue4"))
62 png(filename=plot1.png, width=510, height=300) 63 png(filename=plot1.png, width=510, height=300)
63 print(p) 64 print(p)
64 dev.off() 65 dev.off()
65 66
67 ggsave(plot1.pdf, p)
68
66 data2 = dat[c(1, 5:8),] 69 data2 = dat[c(1, 5:8),]
67 70
68 data2 = data2[,names(data2)[grepl("\\.x", names(data2))]] 71 data2 = data2[,names(data2)[grepl("\\.x", names(data2))]]
69 names(data2) = gsub(".x", "", names(data2)) 72 names(data2) = gsub(".x", "", names(data2))
70 73
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")) 100 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")) 101 #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) 102 png(filename=plot2.png, width=480, height=300)
100 print(p) 103 print(p)
101 dev.off() 104 dev.off()
105
106 ggsave(plot2.pdf, p)
102 107
103 data3 = dat[c(5, 6, 8, 17:20),] 108 data3 = dat[c(5, 6, 8, 17:20),]
104 data3 = data3[,names(data3)[grepl("\\.x", names(data3))]] 109 data3 = data3[,names(data3)[grepl("\\.x", names(data3))]]
105 names(data3) = gsub(".x", "", names(data3)) 110 names(data3) = gsub(".x", "", names(data3))
106 111
136 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black")) 141 #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) 142 png(filename=plot3.png, width=480, height=300)
138 print(p) 143 print(p)
139 dev.off() 144 dev.off()
140 145
146 ggsave(plot3.pdf, p)
141 147
142 148
143 149
144 150
145 151
167 173
168 174
169 175
170 176
171 177
178