User: bhanu.chandra1

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Posts by bhanu.chandra1

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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, Thank you! It is working now. Regards, Bhanu ...
written 10 months ago by bhanu.chandra150
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Comment: C: Gene set enrichment analysis with logFC and PValue
... Hi h.mon, In the hyperlink provided, it is written as "signed fold change * -log10pvalue" In the above-mentioned comment, the following is used: x$logP/x$fcsign Are both of them are similar? ...
written 10 months ago by bhanu.chandra150
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Thank you Ram :). I will take it as a learning experience. ...
written 10 months ago by bhanu.chandra150
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... # set the base colour as 'black' keyvals <- rep('#000000', nrow(res_A_W_lfc)) # set the base name/label as 'NS' names(keyvals) <- rep('NS', nrow(res_A_W_lfc)) # modify keyvals for variables with fold change > 1.5 keyvals[which(res_A_W_lfc$log2FoldChange > ...
written 10 months ago by bhanu.chandra150 • updated 10 months ago by RamRS28k
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, I frequently face the following error: Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), : Viewport has zero dimension(s) Can you please suggest on how to rectify it? ...
written 10 months ago by bhanu.chandra150 • updated 10 months ago by RamRS28k
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, Thank you for the response. Now I could use the colCustom parameter and do the required by following the examples in the Github. Thank you again! ...
written 10 months ago by bhanu.chandra150
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Ram, I am sorry, I thought the earlier comment was a different thread. i will delete one of the two. ...
written 11 months ago by bhanu.chandra150
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, I have two questions: 1. When I plot with results object (after shrinkage), the number of genes (visible on the plot) passing the cutoff criteria are relatively less when compared to the plot with results object (without shrinkage). The graph looks nice with shrinkage and much more dispe ...
written 11 months ago by bhanu.chandra150
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, Thank you for the response. Both of your suggestions worked :) pointSize = c(ifelse(abs(res$log2FoldChange)>2 & res$padj>0.05, > 8, 1)) I guess, there should not be '>' before 8. Thank you! ...
written 11 months ago by bhanu.chandra150 • updated 10 months ago by RamRS28k
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, EnhancedVolcano package was really helpful. I have two doubts: 1. when I used the below option legend=c('NS','Log (base 2) fold-change','P value', 'P value & Log (base 2) fold-change') it has printed Log (base 2) but not the Log2 (subscript). May I know how to do it. 2. when I ...
written 11 months ago by bhanu.chandra150

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