heat map code not working

Question

[Patricia]

hii everyone,

I am trying to create a heatMAP from my RNAseq data but it seems that this code is using ALL of the genes, so I get a heat map that is pretty much impossible to read. Is there a way to filter and only use for example the significant values? Or even select which genes I want to include in the heat map?

library(DESeq2)
library(ggplot2)
library(ComplexHeatmap)

sigs2h <- read.csv("deseq2_analysis/DFE_condition_pri_vs_Control2h.csv")
sigs2h

mat <- counts(dds, normalized = T)

mat.z <- t(apply(mat,1,scale))
colnames(mat.z) <- rownames("samples_round2h.txt")

#mat.z [is.na(mat.z)] = 0 
mat.z[is.na(mat.z)] = 0
Heatmap(mat.z, cluster_rows = T, cluster_columns = T, column_labels = colnames(mat.z), name ="Z=score")

Answer 1

[Asaf]

1. Usually, it's better to use the output of vst rather than plotting the counts after scale, it will keep the variance constant.

2. If you want to select the genes from a list you should subset the matrix, simply run:

   glist <- # A list of genes

   mat.s <- mat[, glist]

   Heatmap(mat.s ...