Best tools for Visualing RNASeq data

Question

[Sreeraj Thamban]

Helloo biostars, I want visualise/plot the expression pattern of a set genes from my RNASeq data. Which are the best R packages or other softawares to do so? I came accross maSigPro and impulseDE but was not impressed by them. Thanks in advance

[WouterDeCoster]

It's unclear what the message is of the plot you want to make. Are you comparing two groups for the expression of one gene?

[Sreeraj Thamban]

Hi Coster, I have a group of genes which are involved in a common pathway. I wanted to plot the overall trend of their expression pattern between treated and untreated samples.

[Jake Warner]

Sounds like maybe you want to make an MA plot or a volcano plot? In that case DEseq2 has some built in functions. Otherwise you can make your own MA plot using base R graphics or ggplot.

[WouterDeCoster]

In addition, for comparing just one gene (or a few) between multiple conditions violin plots are also pretty neat.

[cpad0112]

Then, i guess, you can overlay the expression pattern (of the the pathway members) over KEGG pathway. There are bioconductor packages to do this.

[Kristoffer Vitting-Seerup]

Why not simply a violin plot log2 fold chages for all genes in that pathway?

Answer 1

[Kevin Blighe]

You may want to take a look at my answer here, which deals specifically with RNA-seq gene signatures and how best to evaluate them: A: Resources for gene signature creation

If you literally just want to look at patterns of gene expression, then why not use:

heatmap.2 package

complexheatmap package

corrplot

image host

Answer 2

[Hussain Ather]

heatmaps in matplotlib or seaborn might be helpful