Dear BioStar Leaders,
I am using plotHeatmap function from R's scater 1.14.6 package, and my Differentially expressed genes list is 110 genes, and my HeatMap shows gene symbols/names where they overlap with each other, and they are not legible.
Is there a parameter in plotHeatmap function of scater package, that I can use to change or reduce the size of gene names displayed on my heat map ? (or) if I can scale my heat map to make my genes clearly visible ?
My Single Cell RNA Seq Heat Map is here :
•
written
by
gsr9999
1 answer
Pass the fontsize_row parameter to your plotHeatmap call and adjust accordingly. May have to play around with it to get the right size.
That function uses pheatmap on the backend, and passes extra parameters not recognized by plotHeatmap directly to the pheatmap call if you want to adjust further.
@gsr9999
Hello, Unrelated question! How do you group based on your cluster and batch in plotHeatmap function.
Thank you
You are more likely to get an answer by posting a new question with appropriate details rather than tacking on to an old thread.
Regardless, the annotation_col parameter is what you need to provide.
As an aside, dittoHeatmap from the dittoSeq package is made to work with single cell data and is easier to use.
Log in to answer this question.
-
Colsep for dendrogram and ColSideColors in heatmap.2
written by fabian •
-
use gene symbol in heatmap instead of ensemble geneID
written by Claire •
-
shows the expression of genes in specific cell types in Heatmap
written by Maria17 •
-
Can I enrich a gene expression signature derived from single cell RNA-Seq in a bulk RNA-Seq data se…
written by miherbert •
-
impulseDE2 result table
written by Josephine •
-
How to scale data for scater plotHeatmap function similar to Seurat?
written by TJ •
-
Feature selection for differential analysis
written by wo_li •
-
Is there a data base, tool or method I can use to find out which of my genes code for cytokine rece…
written by charlesgwellem •
-
Converting a function to work with another package
written by Za
-
gene expression level of a specific gene-set from cuffdiff output
written by Giuseppe •
Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)
Got it Thanks, Now I have the image address uploaded