Mercurial > repos > davidvanzessen > plotting_merged
changeset 45:2c6d04fa10f4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 25 Nov 2013 08:30:26 -0500 |
| parents | 20763d15d641 |
| children | a2db27f58627 |
| files | RScript.r |
| diffstat | 1 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/RScript.r Fri Nov 22 08:16:43 2013 -0500 +++ b/RScript.r Mon Nov 25 08:30:26 2013 -0500 @@ -30,6 +30,11 @@ test = test[test$Sample != "",] +if("Replicate" %in% colnames(test)) +{ + test$SRID = do.call(paste, c(test["Sample", "Replicate"], sep = "-")) +} + test$Top.V.Gene = gsub("[*]([0-9]+)", "", test$Top.V.Gene) test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene) test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene) @@ -126,7 +131,7 @@ img = ggplot() + geom_tile(data=dat, aes(x=factor(reorder(Top.D.Gene, chr.orderD)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=relLength)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + - scale_fill_gradient(low="gold", high="blue", na.value="white") + + scale_fill_gradient(low="gold", high="blue", na.value="white", limits=c(0,1)) + ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + xlab("D genes") + ylab("V Genes") @@ -161,7 +166,7 @@ img = ggplot() + geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=relLength)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + - scale_fill_gradient(low="gold", high="blue", na.value="white") + + scale_fill_gradient(low="gold", high="blue", na.value="white", limits=c(0,1)) + ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + xlab("J genes") + ylab("V Genes") @@ -193,7 +198,7 @@ img = ggplot() + geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), y=factor(reorder(Top.D.Gene, chr.orderD)), fill=relLength)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + - scale_fill_gradient(low="gold", high="blue", na.value="white") + + scale_fill_gradient(low="gold", high="blue", na.value="white", limits=c(0,1)) + ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + xlab("J genes") + ylab("D Genes")