I have been struggling with this problem particularly for the similar expression gene graph where I can see only the tracking id's XLOC... which actually even do not match with any of the id's I got after performing k-means clustering (I did this to choose possible candidate genes).
It would be useful to know how to change this for other graphs too.
Thank you!
Hi,
I assume you are taking about the heatmap for digital gene expression, if so than you there are two way to do it. First you have to find the command of R-script in cummerbund and chose desired field from the expression count matrix. Which is laborious and require too much effort. Second is just create this plot via R interface by using set command lines.
Use these links for more details:
http://sourceforge.net/projects/heatmapgenerator/
https://github.com/slzhao/heatmap3
http://nihlibrary.campusguides.com/dataservices/heatmaps
http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/
http://www.r-bloggers.com/r-heatmaps-with-gplots/
Hope you find it useful.
Good luck.
Dear Gopal,
Thank you for your answer!
Actually, the heatmaps and bar graphs were the ones where I got gene names depicted! I suppose, this may be because of the highlited command:
> gene_diff_data sig_gene_data up_gene_data 2))
> geneids myGenes jpeg("heatmap5.jpeg")
> csHeatmap(myGenes, cluster="both")
I have been trying to use something like this for the similar gene expression graphs, but it never worked. I tried several approaches from the blogs, but none of those worked too, that is why I am hoping that someone with experience here would know specifically, how to solve the problem.
Dear Lishuang,
Thank you so much for your response!
This seems to be quite limiting problem since if these IDs do not reliably represent particular genes, the output is inconclusive... But the weird thing is that for some graphs like heatmaps this is not a problem and gene names are given right away.
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