This is a test version of Biostars. For the public version, visit https://www.biostars.org.
gplot heatmap: row names as numbers rather than gene names

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 
heatmap.2(data1, trace = "none", density = "none", col = bluered(20),cexRow = 1, margins = c(10,12), Rowv= FALSE,Colv = FALSE)

I have tried fallowing code, but didn't help

row.names<-row.names(data1[1,])

Kindly help me Thanking you in Advance

r
• 1,481 views • link
updated by h.mon h.mon • written by challagandla.anil • challagandla.anil

1 answer

You should write instead:

row.names(data1) <- EZ2_sorted[,1]

Or even better, define row names when you read the csv file using read.csv instead of read_csv:

EZ2_Sorted <- read.csv("EZ2 Sorted.csv", row.names=1)
• 0 views • link
written by Asaf Asaf

Vooow, that was quick and it worked perfectly. Many Thanks to you :).

• 0 views • link
written by challagandla.anil • challagandla.anil

Log in to answer this question.

More posts like this
  • Heatmap.2
    written by Dk • Dk
    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), …
  • 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. …
  • heatmap in R
    written by Rob • Rob
    Hello friends I want to make a heatmap for gene data in R. this is the code: geneExp <- read.table("file.txt", header=T, sep="\t") head(geneExp) # Extract …
  • 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 …
  • giving a color to null values on heatmap2
    written by demoraesdiogo2017 • demoraesdiogo2017
    Hello I'm using the following code to generate a heatmap for my data, like this library(gplots) getwd() row.names(fold_change_cuttoff_at_2_cuttoff_at_2) <- fold_change_cuttoff_at_2$Gene y <-data.matrix(fold_change_cuttoff_at_2) y <- y[1:2162, …
  • How to cluster in heatmap.2
    written by Björn • Björn
    How to cluster heatmap using different distance matrix (Manhattan or Euclidean) and split column or row-wise in following command heatmap.2(lcpm, Colv=FALSE, dendrogram="row",labRow = y2$genes$genes, Rowv …
  • obtain from the gene names from heat map.2
    written by nakanomasayuki265 • nakanomasayuki265
    I am trying to know gene names from a heatmap made by heatmap. 2. Since I have many genes, the gene names (row labels) are …
  • 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, …
  • 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 …