Hello, I have a matrix of the number of significant SNPs for different traits from different genomes. I want to show this information in the heatmap. So, I used the datamatrix and plotted the attached heatmap using the following code:
pheatmap(data_frame,cluster_rows = F, scale = "row",color = (colorRampPalette(c("navy", "white", "firebrick3"))(20),cluster_cols = F, fontsize_number = 8))
However, this does not show the actual information, rather it scales the number of SNPs and somehow over-represent the data. If I use
scale="none" then I get a very bad heatmap with very little differentiation according to the color. The problem is that I have big differences in my data. The number of SNPs is ranged from 1 to 180.
Is there any way to plot a heatmap by keeping the original data and use a log color scale to better visualize the data?
Please let me know.