Hi Can any one show some good dot-plots showing the differential gene expression analysis for up/down regulated genes. I tried cluster profile, its not working for my data. Some other way how to generate good interpretation dotplots. Suggestions.
The question is a bit ambigous. What do you want to plot precisely?
For instance you can use
ggplot2 to do the doplot if you retrieve and tidy the data properly. Although depending on what do you want to plot on the dotplot (x and y axis) or providing an example together with the example data that you have, it's hard to elaborate more.
The following code makes a dotplot on the top n differently expressed genes. Though this is only the plot. Before I retrieved the most differently expressed gene names from a differently expressed gene table (obtained with
DESeq2) and I retrieved the normalized gene counts for these gene names (from a gene expressed table normalized) in order to plot the gene normalized counts per sample of the top n differently expressed genes. The y-axis is scaled by
log10 and the different top n genes appeared by
ggplot( dge_df, aes( x = Samples, y = Counts, color = Condition, fill = Condition ) ) + geom_point() + facet_wrap( ~ GeneID ) + scale_y_log10() + ylab("Counts") + #theme_bw() + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) + ggtitle( paste0("Top ", topUp_len, " upregulated genes") )
Have a look into the result:
I hope this helps,