Mercurial > repos > davidvanzessen > test_plotting_merged
changeset 5:021d293121bb draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 14 Oct 2013 09:49:29 -0400 |
| parents | 10cfa5e9186e |
| children | f9a657db7af5 |
| files | RScript.r |
| diffstat | 1 files changed, 12 insertions(+), 3 deletions(-) [+] |
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--- a/RScript.r Mon Oct 14 08:12:41 2013 -0400 +++ b/RScript.r Mon Oct 14 09:49:29 2013 -0400 @@ -108,8 +108,9 @@ plotVD <- function(dat){ + #dat = dat[order(dat[,8],dat[,9]),] img = ggplot() + - geom_tile(data=dat, aes(x=factor(Top.D.Gene), y=factor(Top.V.Gene), fill=log)) + + geom_tile(data=dat, aes(x=factor(reorder(Top.D.Gene, chr.orderD)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=log)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_fill_gradient(low="gold", high="blue", na.value="white") + ggtitle(unique(dat$Sample)) + @@ -128,6 +129,8 @@ completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE) completeVD$Length = as.numeric(completeVD$Length) completeVD$log = log(completeVD$Length) +completeVD = merge(completeVD, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) +completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) #completeVD$log[is.na(completeVD$log)] = 0 l = split(completeVD, f=completeVD[,"Sample"]) @@ -136,8 +139,9 @@ plotVJ <- function(dat){ + #dat = dat[order(dat[,8],dat[,9]),] img = ggplot() + - geom_tile(data=dat, aes(x=factor(Top.J.Gene), y=factor(Top.V.Gene), fill=log)) + + geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=log)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_fill_gradient(low="gold", high="blue", na.value="white") + ggtitle(unique(dat$Sample)) + @@ -155,13 +159,16 @@ completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) completeVJ$Length = as.numeric(completeVJ$Length) completeVJ$log = log(completeVJ$Length) +completeVJ = merge(completeVJ, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) +completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) #completeVJ$log[is.na(completeVJ$log)] = 0 l = split(completeVJ, f=completeVJ[,"Sample"]) lapply(l, FUN=plotVJ) plotDJ <- function(dat){ + #dat = dat[order(dat[,8],dat[,9]),] img = ggplot() + - geom_tile(data=dat, aes(x=factor(Top.J.Gene), y=factor(Top.D.Gene), fill=log)) + + geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), y=factor(reorder(Top.D.Gene, chr.orderD)), fill=log)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_fill_gradient(low="gold", high="blue", na.value="white") + ggtitle(unique(dat$Sample)) + @@ -179,6 +186,8 @@ completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) completeDJ$Length = as.numeric(completeDJ$Length) completeDJ$log = log(completeDJ$Length) +completeDJ = merge(completeDJ, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) +completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) #completeDJ$log[is.na(completeDJ$log)] = 0 l = split(completeDJ, f=completeDJ[,"Sample"]) lapply(l, FUN=plotDJ)