No points in plotGenes

[dosshra]

Hello,
I an running this script:
library(ggplot2) lsgplotsGenes <- plotGenes( vecGeneIDs = NULL, scaNTopIDs = 200, objectImpulseDE2 = objectImpulseDE2, boolMultiplePlotsPerPage=T, boolCaseCtrl = T, dirOut = '/data//home//yr19/', strFileName = 'trend_plot_3.pdf', vecRefPval = NULL, strNameRefMethod = NULL)

In this environment:
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
ImpulseDE2_1.10.0

I am getting the plots with only the trend lines but without the points of the individual samples.
Thank you
Hanan.

[davidsebfischer]

Hi Hanan, this is probably due to some plot simplification = visual acessibility default, if you want to change that you might need to engineer the plotting function plotGenes a bit, your plot may be overly crowded though.

[dosshra]

Thank you David for the response. I have 42 samples, I do no think it will be overly crowded. Can you give a hint how to engineer plotGenes?
Thank you

[davidsebfischer]

Quickest fix would likely be to just superimpose points with ggplot2 onto the figure, you can check out here what these expression values would be

ImpulseDE2/R/srcImpulseDE2_plotGenes.R

Line 190 in 47db614

if (boolSimplePlot) {

[dosshra]

I found the problem. My objectImpulseDE$dfAnnotation did not have the sample names as row names. Therefore, the code in plotGenes:
dfRaw <- data.frame( normCounts = get_matCountDataProc( obj=objectImpulseDE2)[id,vecSamples]/ get_vecSizeFactors(objectImpulseDE2)[vecSamples], time = dfAnnot[vecSamples, ]$Time, Batch = dfAnnot[ vecSamples, get_vecConfounders(obj=objectImpulseDE2)[1]], Condition = dfAnnot[vecSamples, ]$Condition)
resulted in NAs in the condition and time columns of dfRaw and geom_point was not plotted.