pheatmap breaks
Hi Adrian,
I had to add an extra color, but this might do what you want:
chxx<-matrix(runif(100,-3.32,4.422),nrow=10)
chxx.cut<-as.numeric(cut(chxx,breaks=c(-3.5,-1.96,-1,0,1,1.96,5)))
chxx.col<-c("#0000FF","#8888FF","#AAAAFF","#FF8888","#FFAAAA",NA)[chxx.cut]
library(plotrix)
chxx_highcol<-color.scale(chxx[chxx>1.96],extremes=c("#FFAAAA","#FFFFFF"))
chxx.col<-matrix(chxx.col,nrow=10)
chxx.col[is.na(chxx.col)]<-chxx_highcol
color2D.matplot(chxx,cellcolors=chxx.col,show.values=TRUE)
Jim
On Sat, Aug 20, 2016 at 7:22 AM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
Hi group:
I tried multiple times cannot understand the breaks to work for my heatmap.
I am using following way:
pheatmap(chxx,
cluster_cols=FALSE,
annotation_col=annotcols,
annotation_colors=anno_colors,
col=colorRampPalette(c("dark blue", "white", "#ff0000"))(34),
show_colnames=F)
max(chxx)
[1] 4.421862
min(chxx)
[1] -3.324021 I want to plot anything above 1.96 as red, anything below -1.96 as blue 1.195 as pink and 0 - 0.99 as gradient of white pink. similarly, < -1.96 as blue, values greater than -1.96 less that -1 gets light blue and 0 to -0.99 get white gradient to blue. there will be 7 breaks < - 1.96--- - 1- -.99---- 0 ------0.99-1---1.96---->1.96 how can I define the breaks. appreciate your help. Thanks in advance. Adrian
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.