Question: how to plot heat map
0
gravatar for raya.girish
3.0 years ago by
raya.girish20
raya.girish20 wrote:

Hello All if my question is very basic please bear with me because heat map i am leaning. I have sample control vs test with 4000 gene . I took the fpkm value of control and test both in excel sheet along with that i also added the gene name in first column. So my first column is gene name 2nd column is fpkm from control 3column is fpkm from test(this file is one which has no significant or FC filter i means it contain all the genes.) i am trying to generate heatmap using R as of now i tried this command:

a <- read.csv("/home/Desktop/heatmap.csv",sep=",",header=true)
b <- as.matrix(a[,2:3]) 
heatmap(b,Rowv=TRUE,col=heat.colors(256),cexCol =1.0,margins=c(10,20),offsetRow =5,scale="row",dendrogram="column")

the above command has generated heatmap but the yaxis that is what i assume are gene name the not visible i means just one dark colour line thats it. how to go about i am not sure please help.

heatmap geneexpression rnaseq • 1.8k views
ADD COMMENTlink modified 7 months ago by srgk26ster10 • written 3.0 years ago by raya.girish20
1

Can you post the output of head /home/Desktop/heatmap.csv # on command line

or head(a) # in R

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by geek_y10k
3

If you plot 4000 genes you will not be able to read the gene names from the resulting plot labels, the font size will be too small and the labels will overlap, you will only be able to read the names if you plot only the top few genes.

There is another heatmap command in R, heatmap.2 from the gplots package.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by mastal5112.0k
0
gravatar for Alex
3.0 years ago by
Alex30
America
Alex30 wrote:

maybe you will like HemI ,it's very convenient

ADD COMMENTlink written 3.0 years ago by Alex30

What is this Heml? Can you provide the link?

ADD REPLYlink written 3.0 years ago by venu6.3k

http://hemi.biocuckoo.org/

ADD REPLYlink written 3.0 years ago by Alex30
0
gravatar for srgk26ster
7 months ago by
srgk26ster10
srgk26ster10 wrote:

HI! I appreciate that this has been a long time since your question, but you or anyone else reading this may be interested in this. I just developed a Julia-based GUI tool to plot heatmaps based on Python's Seaborn package. Just 10-15 min to get it running. Very minimal/no coding is required for this. Just need to click to input .xlsx/.csv/.txt files and a heatmap would be produced. At the minute, only heatmaps are supported. In the near future, additional plotting types and functionalities will be supported. This is the link with the full information and instruction:

https://github.com/srgk26/easy_plotting.app

ADD COMMENTlink written 7 months ago by srgk26ster10
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