Mercurial > repos > davidvanzessen > plotting_merged

comparison RScript.r @ 37:16fe6233f90e draft

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author davidvanzessen
date Fri, 08 Nov 2013 06:54:21 -0500
parents b3c97b26db60
children 6e490e056fc4
comparison
equal deleted inserted replaced
36:b3c97b26db60 37:16fe6233f90e
113 113
114 plotVD <- function(dat){ 114 plotVD <- function(dat){
115 img = ggplot() + 115 img = ggplot() +
116 geom_tile(data=dat, aes(x=factor(reorder(Top.D.Gene, chr.orderD)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=log)) + 116 geom_tile(data=dat, aes(x=factor(reorder(Top.D.Gene, chr.orderD)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=log)) +
117 theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 117 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
118 scale_fill_gradient(low="gold", high="blue", na.value="white", limits=c(0, maxVD)) + 118 scale_fill_gradient(low="gold", high="blue", na.value="white") +
119 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat[!is.na(dat[,4]),][4]) ,")", sep="")) + 119 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat[!is.na(dat[,4]),][4]) ,")", sep="")) +
120 xlab("D genes") + 120 xlab("D genes") +
121 ylab("V Genes") 121 ylab("V Genes")
122 122
123 png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) 123 png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name)))
124 print(img) 124 print(img)
125 dev.off() 125 dev.off()
126 } 126 }
127 127
128 VandDCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.D.Gene", "Sample")]) 128 VandDCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.D.Gene", "Sample")])
129
130
131
132
133 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name, Sample = unique(test$Sample)) 129 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name, Sample = unique(test$Sample))
134 130
135 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE) 131 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE)
136 completeVD$Length = as.numeric(completeVD$Length) 132 completeVD$Length = as.numeric(completeVD$Length)
137 completeVD$log = log(completeVD$Length) 133 completeVD$log = log(completeVD$Length)
138 maxVD = max(subset(completeVD, !is.na(completeVD$log), "log"))
139 completeVD = merge(completeVD, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) 134 completeVD = merge(completeVD, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
140 completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) 135 completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
141 #completeVD$log[is.na(completeVD$log)] = 0 136 #completeVD$log[is.na(completeVD$log)] = 0
142 l = split(completeVD, f=completeVD[,"Sample"]) 137 l = split(completeVD, f=completeVD[,"Sample"])
143 138