heat map code not working
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")
• 968 views
•
link
updated
by
GenoMax
•
written
by
Patricia •
•
written
by
Patricia •
1 answer
- Usually, it's better to use the output of
vstrather than plotting the counts after scale, it will keep the variance constant. 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 ...
Log in to answer this question.
More posts like this
-
Error with pheatmap - 'from' must be a finite number
written by vmpsb •
-
Help me with Heatmap
written by vmpsb •
-
DESeq2 heatmap with low baseMean values
written by Ahmed •
-
How to label only a few genes of interest in heatmap of bulk RNA-seq
written by Chris •
-
circular heatmap in R Shiny
written by logbio •
-
color key heatmap
written by kalyani •
-
heatmap color key
written by kalyani •
-
boxplot issue
written by kalyani •
-
heatmap in R
written by Rob •
-
heatmap using DESeq2
written by sumithrasank75
