This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Heatmap.2

Hi everyone, I am trying to graph a heatmap for my DEGs data but I encountered some errors. This is my code:

heatmap.2(diffGenes, 
          Rowv=as.dendrogram(clustRows), 
          Colv=as.dendrogram(clustColumns),
          RowSideColors=module.color,
          col=myheatcolors, scale='row', labRow=NA,
          density.info="none", trace="none",  
          cexRow=1, cexCol=1, margins=c(8,20))

However, I got the error message:

Error in plot.new() : figure margins too large

Also, for the packages, I am using:

library(tidyverse)
library(gplots)
library(RColorBrewer)

I tried to look it up how to fix it but I couldn't figure out. Please help me out, thank you guys!

heatmap.2 r degs
• 2,248 views • link
updated by Ram Ram • written by Dk • Dk

1 answer

The RStudio plotting window is too small. Save it to a file, either pdf or png and then view it.

• 0 views • link
written by ATpoint ATpoint

Yes, it works now! Thank you!!

• 0 views • link
written by Dk • Dk

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.

upvote_bookmark_accept

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this
  • No color key in my heatmap with heatmap2.
    written by Riku • Riku
    Dear all, I would like to output the heat map with colorkey on top. However, colorkey will not be displayed when using the following command. …
  • color gradient for heatmap2
    written by jtehmsen • jtehmsen
    Hello, I'd like to create a continuous gradient of warm colors (e.g., yellow-orange-red) from the values 4-9 using heatmap2. Can anyone please suggest code to …
  • Missing a row name in Heatmap.2
    written by francesca3 • francesca3
    Hi, I use heatmap.2 (from ggplots) to produce heatmaps. Sometimes I notice that I miss a row name... It could be the first row, but …
  • gplot heatmap: row names as numbers rather than gene names
    written by challagandla.anil • challagandla.anil
    My data structure: Firts Column is Gene_ID library(RColorBrewer) library(heatmap.plus) library(gplots) EZ2_Sorted <- read_csv("EZ2 Sorted.csv") data1<-as.matrix(EZ2_Sorted[,2:7]) # 1st column gene ID #I have total 8 columns …
  • Why can't I reproduce the same heat map
    written by Za Za
    Hi, Long time I am trying to produce figure 1A in this link but I always plot something weird like this In paper says they …
  • Making a heat map more clear
    written by Za Za
    Hi, I have plotted log normalised data in a heatmap as this picture but how I can make the dots more clrear and darker please? …
  • Sorted hetamap using R
    written by #### ####
    I want to generate the sorted heatmaps based on the expression, what function I have to use to get the sorted heatmap based on expression, …
  • Helping with heatmap
    written by M K M K
    I have a CSV files contains the regression coefficients with their p-values for 5 variables and I want to plot a heatmap in R for …
  • R stat heatmap problem
    written by sparrowquality • sparrowquality
    I am using R for cluster analysis visualized by heatmap. Previously it worked perfectly, but reinstalling the software (and the whole system) started to bring …
  • Removing White Lines In Heatmap
    written by Woa Woa
    <p>Hello all,</p> <p>I'm trying to plot a heatmap using the heatmap.2 function from the 'Gplots' package.I'm getting some unwanted white lines separating some of the …