[Patchwork-commits] r93 - in pkg: patchwork/R patchworkCG/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 15 16:29:40 CET 2012
Author: sebastian_d
Date: 2012-02-15 16:29:39 +0100 (Wed, 15 Feb 2012)
New Revision: 93
Modified:
pkg/patchwork/R/karyotype.r
pkg/patchwork/R/karyotype_chroms.r
pkg/patchwork/R/karyotype_chromsCN.r
pkg/patchworkCG/R/CG_KaCh.r
pkg/patchworkCG/R/CG_KaChCN.r
pkg/patchworkCG/R/CG_karyotype.r
Log:
Updated color gradient scales and method for patchwork and patchworkCG
Modified: pkg/patchwork/R/karyotype.r
===================================================================
--- pkg/patchwork/R/karyotype.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchwork/R/karyotype.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -9,8 +9,8 @@
data(ideogram,package="patchworkData")
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
layout(matrix(1:25,nrow=5,byrow=T), widths=1,heights=1)
@@ -35,11 +35,17 @@
this <- ideogram[ideogram$c==c,]
ix <- chr==this$chr
ix[is.na(ix)]=FALSE
+
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
- col <- rep('#B0B0B070',length(chr))
-
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
Modified: pkg/patchwork/R/karyotype_chroms.r
===================================================================
--- pkg/patchwork/R/karyotype_chroms.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchwork/R/karyotype_chroms.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -10,8 +10,8 @@
#create a color ramp palette to segue the color scheme for plot.
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
ai[is.na(ai)]=0
aix=ai!=0
@@ -38,10 +38,17 @@
mar.default <- c(5,4,4,2) + 0.1
par(mar = mar.default + c(0, 4, 0, 0))
- ix <- chr==this$chr
- col <- rep('#B0B0B070',length(chr))
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ ix <- chr==this$chr
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
+
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
Modified: pkg/patchwork/R/karyotype_chromsCN.r
===================================================================
--- pkg/patchwork/R/karyotype_chromsCN.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchwork/R/karyotype_chromsCN.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -9,8 +9,8 @@
data(ideogram,package="patchworkData")
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
ai[is.na(ai)]=0
aix=ai!=0
@@ -39,10 +39,17 @@
mar.default <- c(5,4,4,2) + 0.1
par(mar = mar.default + c(0, 4, 0, 0))
- ix <- chr==this$chr
- col <- rep('#B0B0B070',length(chr))
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ ix <- chr==this$chr
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
+
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
Modified: pkg/patchworkCG/R/CG_KaCh.r
===================================================================
--- pkg/patchworkCG/R/CG_KaCh.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchworkCG/R/CG_KaCh.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -10,9 +10,12 @@
#create a color ramp palette to segue the color scheme for plot.
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ #colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ #colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
+
ai[is.na(ai)]=0
aix=ai!=0
chr=chr[aix]
@@ -29,7 +32,7 @@
size[length>5000000]=4
size[length>10000000]=5
size[length>20000000]=6
-
+
for (c in 1:24)
{
this <- ideogram[ideogram$c==c,]
@@ -41,9 +44,19 @@
par(mar = mar.default + c(0, 4, 0, 0))
ix <- chr==this$chr
- col <- rep('#B0B0B070',length(chr))
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
+
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
+
+ #col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
+ #col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
Modified: pkg/patchworkCG/R/CG_KaChCN.r
===================================================================
--- pkg/patchworkCG/R/CG_KaChCN.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchworkCG/R/CG_KaChCN.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -7,10 +7,12 @@
#load(paste(packagepath,"/data/ideogram.RData",sep=""))
data(ideogram,package="patchworkCG")
-
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ #Origional
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
+ #colors_chrom = colorRampPalette(c("#6600FF","#CC0000"),space="rgb")
+
ai[is.na(ai)]=0
aix=ai!=0
chr=chr[aix]
@@ -40,10 +42,23 @@
mar.default <- c(5,4,4,2) + 0.1
par(mar = mar.default + c(0, 4, 0, 0))
- ix <- chr==this$chr
- col <- rep('#B0B0B070',length(chr))
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ #Create a list of colors length of chromosome.
+ #Assign color by middle of segment. (pos as an int).
+
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
+
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
+
+ #Origional
+ #col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
+ #col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
Modified: pkg/patchworkCG/R/CG_karyotype.r
===================================================================
--- pkg/patchworkCG/R/CG_karyotype.r 2012-02-15 13:29:40 UTC (rev 92)
+++ pkg/patchworkCG/R/CG_karyotype.r 2012-02-15 15:29:39 UTC (rev 93)
@@ -9,9 +9,12 @@
data(ideogram,package="patchworkCG")
- colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
- colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ #colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
+ #colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+ colors_p <- colorRampPalette(c("#2754e8","#ad09e8"),space="rgb")
+ colors_q <- colorRampPalette(c("#c309e8","#e81e2c"),space="rgb")
+
layout(matrix(1:25,nrow=5,byrow=T), widths=1,heights=1)
aix=ai!=0
@@ -38,10 +41,16 @@
ix <- chr==this$chr
ix[is.na(ix)]=FALSE
- col <- rep('#B0B0B070',length(chr))
-
- col[ix & (pos < this$mid)] <- paste(colors_p(sum(ix & (pos < this$mid))), '70', sep='')
- col[ix & (pos > this$mid)] <- paste(colors_q(sum(ix & (pos > this$mid))), '70', sep='')
+ ix_p = ix & (pos < this$start)
+ ix_q = ix & (pos > this$end)
+ col <- rep('#B0B0B070',length(chr))
+
+ #loc = list of colors
+ loc_p=colors_p(ceiling(this$start/100))
+ loc_q=colors_q(ceiling((this$length - this$end)/100))
+
+ col[ix_p] = paste(loc_p[ceiling(pos[ix_p]/100)],'70',sep='')
+ col[ix_q] = paste(loc_q[ceiling((pos[ix_q]-this$end)/100)],'70',sep='')
plot(c(int[!ix],int[ix]),c(ai[!ix],ai[ix]),
pch=16,
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