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biopet.biopet
Commit 190b7590 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge branch 'develop' into fix-BIOPET-659

parents 0d996e40 11260a4c
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Showing with 6 additions and 4 deletions
biopet-core/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
View file @ 190b7590
......@@ -14,6 +14,7 @@ rownames(heat) <- heat[,1]
heat<- heat[,-1]
heat<- as.matrix(heat)
textMargin <- max(sapply(rownames(heat), nchar)) + 4
colNumber <- 50
col <- rev(colorRampPalette(brewer.pal(11, "Spectral"))(colNumber))
for (i in (colNumber+1):(colNumber+round((dist(range(heat)) - dist(range(heat[heat < 1]))) / dist(range(heat[heat < 1])) * colNumber))) {
......@@ -22,7 +23,7 @@ for (i in (colNumber+1):(colNumber+round((dist(range(heat)) - dist(range(heat[he
col[length(col)] <- "#00FF00"
png(file = outputArg, width = 1200, height = 1200)
heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none", margins = c(12, 12), na.color="#00FF00")
heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none", margins = c(textMargin, textMargin), na.color="#00FF00")
dev.off()
hc <- hclust(d = dist(heat))
......@@ -31,5 +32,5 @@ plot(as.dendrogram(hc), horiz=TRUE, asp=0.02)
dev.off()
png(file = outputArgClustering, width = 1200, height = 1200)
heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(12, 12), na.color="#00FF00")
heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(textMargin, textMargin), na.color="#00FF00")
dev.off()
biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/vcfstats/plotHeatmap.R
View file @ 190b7590
......@@ -14,6 +14,7 @@ rownames(heat) <- heat[,1]
heat<- heat[,-1]
heat<- as.matrix(heat)
textMargin <- max(sapply(rownames(heat), nchar)) + 4
colNumber <- 50
col <- rev(colorRampPalette(brewer.pal(11, "Spectral"))(colNumber))
for (i in (colNumber+1):(colNumber+round((dist(range(heat)) - dist(range(heat[heat < 1]))) / dist(range(heat[heat < 1])) * colNumber))) {
......@@ -22,7 +23,7 @@ for (i in (colNumber+1):(colNumber+round((dist(range(heat)) - dist(range(heat[he
col[length(col)] <- "#00FF00"
png(file = outputArg, width = 1200, height = 1200)
heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none", margins = c(12, 12), na.color="#00FF00")
heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none", margins = c(textMargin, textMargin), na.color="#00FF00")
dev.off()
hc <- hclust(d = dist(heat))
......@@ -31,5 +32,5 @@ plot(as.dendrogram(hc), horiz=TRUE, asp=0.02)
dev.off()
png(file = outputArgClustering, width = 1200, height = 1200)
heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(12, 12), na.color="#00FF00")
heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(textMargin, textMargin), na.color="#00FF00")
dev.off()
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