Labels are not showing in plotVolcano

[kokyriakidis]

Hi @mjsteinbaugh ,

I run an analysis using the DE template and everything works perfectly except the Volcano plot. It cannot show top gene labels

> plotVolcano(object = deseq, i = 1L, ntop = 10L)
→ category_AD_vs_Control (shrunken LFC)
ℹ 34 non-unique gene symbols detected.
ℹ Labeling 10 genes in plot.
Warning message:
Removed 10 rows containing missing values (geom_label_repel). 

Have you any idea why I get missing values? Every other plot (eg. MA) correctly show labels for top genes.

Best, KK

[mjsteinbaugh]

OK thanks I'll check that today

[mjsteinbaugh]

You're right, this appears to be a bug in DESeqAnalysis 0.4.2. I'm working on pushing a fix. Here's a reprex:

packageVersion("DESeqAnalysis")
## [1] ‘0.4.2’
library(DESeqAnalysis)
data(deseq)
plotVolcano(object = deseq, i = 1L, ntop = 10L)
Warning: Removed 10 rows containing missing values (geom_label_repel).

[mjsteinbaugh]

OK this should be fixed in DESeqAnalysis 0.4.3. I'm pushing that recipe update to conda as well.