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jokergoo / EnrichedHeatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
http://jokergoo.github.io/EnrichedHeatmap/
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multiplemEnrichedheatmaps with only line plots #36

Closed Papareddy closed 5 years ago

Papareddy commented 5 years ago

Hello,

I am trying to plot methylation value in differnt tissue types on gene bodies. I normally use deeptools plotProfile function but it doesn't have a smoothening option. So I like Enrichedheatmap for that reason. However I was wondering whether i can plot only the lineplot with out heatmap.

Hope i am making sense. Many thanks, Ranj enrichedheatmap_lineplot

jokergoo commented 5 years ago

Hi, there are two ways:

  1. you can refer to the plot above the section: http://bioconductor.org/packages/devel/bioc/vignettes/EnrichedHeatmap/inst/doc/roadmap.html#toc_7 where you can use add_anno_enriched() to extract the plot which is exactly the same as on top of the heatmap.

  2. Directly plot colMeans(m) where m is the normalized matrix from normalizeToMatrix(). The disadvantage is if you split m in the heatmap, you need to manually split m into m1 and m2, later add lines for colMeans(m1) and colMeans(m2).