Hi Steve, That plot looks to me as though a value-to-color transformation is performed on the logarithm of gene expression. The scale bar can be roughly reproduced like this:
library(plotrix) plot(0,xlim=c(0,3)) gradient.rect(0,-0.1,3,0.1, col=color.scale(seq(0,3,0.1), c(0.7,1,1,1,0.7,0.2), c(0.7,1,0,0,0,0), c(1,0,0,0.1,0.7,0.2))) text(0:3,rep(0.2,3),c(0,10,100,1000)) The horizontal lengths of the stacked bars of the plot can then be adjusted to the number of subjects in a given bin of log gene expressions. A tricky plot, but it can be done in R. Jim On Fri, Nov 5, 2021 at 6:08 PM Stephen HonKit Wong <stephe...@gmail.com> wrote: > > Dear Community, > > I have an example heatmap plot in this link > <https://drive.google.com/file/d/15ePaR0gC2IKXm2gkeGylZ4vM_MEsWyW0/view?usp=sharing> > which was generated by java I believe, I want to make a similar plot in R. > Any clues on how to do it? Thanks. > > The column is a gene, and the rows are different cancer types with > different numbers of patients. The heatmap value represents the expression > value, such as FPKM, which can range from 0 to over several hundreds. > > > Much thanks! > > Steve > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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. ______________________________________________ R-help@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.
