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
heatmap ploting
2 messages · Stephen HonKit Wong, Jim Lemon
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 <stephen66 at 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]]
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