Mercurial > repos > davidvanzessen > plotting_merged

comparison RScript.r @ 29:1c25c75d863d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 30 Sep 2013 05:14:21 -0400
parents e920d28843b6
children 548b3035bbd7
comparison
equal deleted inserted replaced
28:e920d28843b6 29:1c25c75d863d
52 Total = 0 52 Total = 0
53 Total = ddply(PRODFJ, .(Sample), function(x) data.frame(Total = sum(x$Length))) 53 Total = ddply(PRODFJ, .(Sample), function(x) data.frame(Total = sum(x$Length)))
54 PRODFJ = merge(PRODFJ, Total, by.x='Sample', by.y='Sample', all.x=TRUE) 54 PRODFJ = merge(PRODFJ, Total, by.x='Sample', by.y='Sample', all.x=TRUE)
55 PRODFJ = ddply(PRODFJ, c("Sample", "Top.J.Gene"), summarise, relFreq= (Length*100 / Total)) 55 PRODFJ = ddply(PRODFJ, c("Sample", "Top.J.Gene"), summarise, relFreq= (Length*100 / Total))
56 56
57
58 V = c("v.name\tchr.orderV\nIGHV7-81\t1\nIGHV3-74\t2\nIGHV3-73\t3\nIGHV3-72\t4\nIGHV3-71\t5\nIGHV2-70\t6\nIGHV1-69\t7\nIGHV3-66\t8\nIGHV3-64\t9\nIGHV4-61\t10\nIGHV4-59\t11\nIGHV1-58\t12\nIGHV3-53\t13\nIGHV3-52\t14\nIGHV5-a\t15\nIGHV5-51\t16\nIGHV3-49\t17\nIGHV3-48\t18\nIGHV3-47\t19\nIGHV1-46\t20\nIGHV1-45\t21\nIGHV3-43\t22\nIGHV4-39\t23\nIGHV3-35\t24\nIGHV4-34\t25\nIGHV3-33\t26\nIGHV4-31\t27\nIGHV4-30-4\t28\nIGHV4-30-2\t29\nIGHV3-30-3\t30\nIGHV3-30\t31\nIGHV4-28\t32\nIGHV2-26\t33\nIGHV1-24\t34\nIGHV3-23\t35\nIGHV3-22\t36\nIGHV3-21\t37\nIGHV3-20\t38\nIGHV3-19\t39\nIGHV1-18\t40\nIGHV3-15\t41\nIGHV3-13\t42\nIGHV3-11\t43\nIGHV3-9\t44\nIGHV1-8\t45\nIGHV3-7\t46\nIGHV2-5\t47\nIGHV7-4-1\t48\nIGHV4-4\t49\nIGHV4-b\t50\nIGHV1-3\t51\nIGHV1-2\t52\nIGHV6-1\t53") 57 V = c("v.name\tchr.orderV\nIGHV7-81\t1\nIGHV3-74\t2\nIGHV3-73\t3\nIGHV3-72\t4\nIGHV3-71\t5\nIGHV2-70\t6\nIGHV1-69\t7\nIGHV3-66\t8\nIGHV3-64\t9\nIGHV4-61\t10\nIGHV4-59\t11\nIGHV1-58\t12\nIGHV3-53\t13\nIGHV3-52\t14\nIGHV5-a\t15\nIGHV5-51\t16\nIGHV3-49\t17\nIGHV3-48\t18\nIGHV3-47\t19\nIGHV1-46\t20\nIGHV1-45\t21\nIGHV3-43\t22\nIGHV4-39\t23\nIGHV3-35\t24\nIGHV4-34\t25\nIGHV3-33\t26\nIGHV4-31\t27\nIGHV4-30-4\t28\nIGHV4-30-2\t29\nIGHV3-30-3\t30\nIGHV3-30\t31\nIGHV4-28\t32\nIGHV2-26\t33\nIGHV1-24\t34\nIGHV3-23\t35\nIGHV3-22\t36\nIGHV3-21\t37\nIGHV3-20\t38\nIGHV3-19\t39\nIGHV1-18\t40\nIGHV3-15\t41\nIGHV3-13\t42\nIGHV3-11\t43\nIGHV3-9\t44\nIGHV1-8\t45\nIGHV3-7\t46\nIGHV2-5\t47\nIGHV7-4-1\t48\nIGHV4-4\t49\nIGHV4-b\t50\nIGHV1-3\t51\nIGHV1-2\t52\nIGHV6-1\t53")
59 tcV = textConnection(V) 58 tcV = textConnection(V)
60 Vchain = read.table(tcV, sep="\t", header=TRUE) 59 Vchain = read.table(tcV, sep="\t", header=TRUE)
61 PRODFV = merge(PRODFV, Vchain, by.x='Top.V.Gene', by.y='v.name', all.x=TRUE) 60 PRODFV = merge(PRODFV, Vchain, by.x='Top.V.Gene', by.y='v.name', all.x=TRUE)
62 close(tcV) 61 close(tcV)
74 PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE) 73 PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE)
75 close(tcJ) 74 close(tcJ)
76 75
77 pV = ggplot(PRODFV) 76 pV = ggplot(PRODFV)
78 pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) 77 pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
78 pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage")
79 #pV 79 #pV
80 80
81 pD = ggplot(PRODFD) 81 pD = ggplot(PRODFD)
82 pD = pD + geom_bar( aes( x=factor(reorder(Top.D.Gene, chr.orderD)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) 82 pD = pD + geom_bar( aes( x=factor(reorder(Top.D.Gene, chr.orderD)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
83 pD = pD + xlab("Summary of D gene") + ylab("Frequency") + ggtitle("Relative frequency of D gene usage")
83 #pD 84 #pD
84 85
85 pJ = ggplot(PRODFJ) 86 pJ = ggplot(PRODFJ)
86 pJ = pJ + geom_bar( aes( x=factor(reorder(Top.J.Gene, chr.orderJ)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) 87 pJ = pJ + geom_bar( aes( x=factor(reorder(Top.J.Gene, chr.orderJ)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
88 pJ = pJ + xlab("Summary of J gene") + ylab("Frequency") + ggtitle("Relative frequency of D gene usage")
87 #pJ 89 #pJ
88 90
89 #plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2)) 91 #plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2))
90 #plotall 92 #plotall
91 #ggsave(outFile, dpi=125) 93 #ggsave(outFile, dpi=125)
92 94
95
93 png(outFile,width = 1920, height = 1200) 96 png(outFile,width = 1920, height = 1200)
94 print(plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2))) 97 plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2))
95 dev.off() 98 dev.off()
96 99
97 100