Removed 351 rows containing missing values (geom_point)

kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling

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Removed 351 rows containing missing values (geom_point) #5

Closed pkhadkagh closed 5 years ago

pkhadkagh commented 5 years ago

Hi Kevin,

Your package works well for most of what I am trying to do. But I keep getting the following error when I try to make the volcano plot: "Warning message: Removed 351 rows containing missing values (geom_point)" It doesn't seem to be a problem with the axes limits as I changed both of them to accommodate the max and min of both variables. Any idea what might be causing this problem? Thanks!

kevinblighe commented 5 years ago

Hey prasidda, thank you for using EnhancedVolcano! What is the source of your data? Do you know if the test statistics contain missing or infinite values? Some statistical tests will return 'NA' or 'Inf' for genes for which no accurate model can be fit.

kevinblighe commented 5 years ago

I have made changes and these warning messages should no longer appear. They are produced when there are NAs in your data.

Commit: https://github.com/kevinblighe/EnhancedVolcano/commit/f6e8ea696567735887fcf3d3ff734577c1462f9b

pkhadkagh commented 5 years ago

Thanks, Kevin. I did realize that it was indeed NAs in my data giving this error. I was using DeSeq2 data and didn't expect there to be NAs in the p-value column, but there were quite a few when I checked.

kevinblighe commented 5 years ago

No problem. To avail of the new code, you will have to wait until the next Bioconductor release or else downloading the development version of the package via: devtools::install_github("https://github.com/kevinblighe/EnhancedVolcano/")

MichaelPeibo commented 5 years ago

Hi @prasidda @kevinblighe I have some labels not shown gene symbol or id on the plots, is this due to NAs?