Heatmaps

There are several functions you may employ to get heatmaps:
default heatmap, image

heatmap.2 in gplots package
heatplot in made4 Bioconductor package
heatmap_2, heatmap_plus in Heatplus Bioconductor package

So far heatmap.2 in gplots works best. If you want to plot some covariates use heatmap_plus

The easiest way to define a custom colorPalette is

colorRamPalette(colors)(num_of_interpretation)