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I am using R Markdown to graph a volcano plot of genes using the Seurat and EnhancedVolcano packages.

This is my code below. The 'vgm' is a Seurat Object:

#using Seurat to obtain differentially expressed genes between two groups, labelled 4 vs 6    
DEgenes<- Seurat::FindMarkers(vgm[[2]], group.by = "Group", ident.1="4",ident.2="6", min.pct=0.25)

#results stored in a dataframe
head(DEgenes)

Results of the head() function in the code above produces this output: Output dataframe

Next, I proceed to run the following codes:

#installing and loading EnhancedVolcano
devtools::install_github('kevinblighe/EnhancedVolcano')
library(EnhancedVolcano)

#plotting volcano plot between group 4 (called InEx) vs group 6 (called ReA SF)
#For InEx vs ReA SF
EnhancedVolcano(DEgenes,
    lab = rownames(DEgenes),
    x = 'avg_log2FC',
    y = 'p_val_adj',
    ylim = c(0,450),
    title = 'InEx vs ReA SF',
    xlab = bquote(~Log[1]~ '(Fold Change)'),
    ylab = bquote(~-Log[10]~ '(Adj. p)'),
    axisLabSize = 12,
    FCcutoff = 1.493, 
    pCutoff = 10e-40,
    pointSize = 1,
    drawConnectors = TRUE,
    widthConnectors = 0.75,
    colAlpha = 1,
    max.overlaps = 45)

When I run the code chunk above for my figure, it is displayed within the R Markdown output normally as seen below. As seen in this picture, the labels of certain genes are intact and visible:

Normal display of figure within R Markdown

When I want to see it in a new window, I press this button here (circled in purple):

Show in new window button

However, when this new window is opened, the gene labels are not visible anymore like it was before:

Gene labels not visible

I am not sure why the entirety of the plot is not showing up in the new window. Any ideas on having the gene labels visible in the new window would be greatly welcome!

Thanks in advance! I edited this question to make it as reproducible as possible.

Zoya Qaiyum
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  • Pictures don't give me a lot of context. What code did you use? What's in the YAML? It looks like you're new to SO; welcome to the community! If you want great answers quickly, it's best to make your question reproducible. This includes sample data like the output from `dput()` or `reprex::reprex()`, the programming code, along with any libraries you are using. Check it out: [making R reproducible questions](https://stackoverflow.com/q/5963269). – Kat Jun 12 '23 at 23:34
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    @Kat my apologies, I have edited the question to make it as reproducible as possible. – Zoya Qaiyum Jun 13 '23 at 00:08

0 Answers0