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comparison RScript.r @ 24:41ac5d41cbe3 draft

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author davidvanzessen
date Mon, 30 Sep 2013 03:41:11 -0400
parents 294cb9f3563d
children 10522dec2d35
comparison
equal deleted inserted replaced
23:294cb9f3563d 24:41ac5d41cbe3
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 merged = rbind(PRODFV, PRODFD, PRODFJ)
58 57
59 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") 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")
60 tcV = textConnection(V) 59 tcV = textConnection(V)
61 Vchain = read.table(tcV, sep="\t", header=TRUE) 60 Vchain = read.table(tcV, sep="\t", header=TRUE)
62 PRODFV = merge(PRODFV, Vchain, by.x='Top.V.Gene', by.y='v.name', all.x=TRUE) 61 PRODFV = merge(PRODFV, Vchain, by.x='Top.V.Gene', by.y='v.name', all.x=TRUE)
89 88
90 #plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2)) 89 #plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2))
91 #plotall 90 #plotall
92 #ggsave(outFile, dpi=125) 91 #ggsave(outFile, dpi=125)
93 92
94 sink(outFile, append=FALSE, split=FALSE) 93 sink(outFile, append=TRUE, split=FALSE)
95 merged 94 PRODFV
95 PRODFD
96 PRODFJ
96 unlink(outFile) 97 unlink(outFile)
97 98
98 #png(outFile,width = 1920, height = 1200) 99 #png(outFile,width = 1920, height = 1200)
99 #print(plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2))) 100 #print(plotall = grid.arrange(pV, arrangeGrob(pD, pJ, ncol=2), ncol=1, widths=c(1,1.2)))
100 #dev.off() 101 #dev.off()