When running the circle_dat command from the GOplot package, I'm running into an issue that I can't seem to solve. I have two data files: one for my GO analysis results (GoList), and one for my DEG gene list/analysis results (genelist), as specified in the github for the GOplot package.
I'm trying to generate a GOcircle plot. Here's the code I've ran:
> genelist <- read.csv('2hGeneComparison2.csv')
> GoList <- read.csv('ResultsGo3.csv')
> circ <- circle_dat(GoList, genelist)
> GOCircle(circ)
head(circ) returns the following, where you can see I'm getting NA values for logFC and zscore columns:
head(circ)
category ID term count
1 BP GO:0070371 ERK1 and ERK2 cascade 1
2 BP GO:0070372 regulation of ERK1 and ERK2 cascade 1
3 BP GO:0030217 T cell differentiation 1
4 BP GO:0060326 cell chemotaxis 1
5 BP GO:0032680 regulation of tumor necrosis factor production 1
6 BP GO:0002237 response to molecule of bacterial origin 1
genes
1 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
2 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
3 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
4 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
5 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
6 (List of ENSEMBL ID's that I couldn't get to copy and paste properly here)
logFC adj_pval zscore
1 NA 2.99e-09 NA
2 NA 7.23e-09 NA
3 NA 6.03e-07 NA
4 NA 7.28e-07 NA
5 NA 7.28e-07 NA
6 NA 7.28e-07 NA
But I'm providing appropriate data for this in the input data files, as seen in head(genelist)
ID baseMean logFC lfcSE stat pvalue adj.P.Val
1 ENSMUSG00000000555 194.8234 0.8937636 0.25189607 3.548144 3.879560e-04 1.301399e-02
2 ENSMUSG00000000686 41.1447 -0.6175972 0.37424955 -1.650228 9.889623e-02 2.998447e-01
3 ENSMUSG00000000982 116.3638 5.7609094 0.75933093 7.586823 3.280000e-14 1.860000e-11
4 ENSMUSG00000001034 635.4174 -0.6153160 0.13473524 -4.566853 4.950000e-06 5.475510e-04
5 ENSMUSG00000001473 370.8013 0.7989403 0.19145612 4.172968 3.010000e-05 2.216721e-03
6 ENSMUSG00000001627 3310.3776 0.7071353 0.09953138 7.104646 1.210000e-12 5.340000e-10
I don't get an error return on this code - it successfully runs and outputs a figure. The issue is the the figure isn't mapping the genes to the GO terms on the GO circle ie. it isn't reading fold changes or zscores to plot onto the graph. Here's an image:
This is clearly an issue within my two data files somewhere, but I've set them up according to the GOplot package github page, so I'm really not sure where I've gone wrong. Does anyone know what exactly would cause such an issue with the plotting function?
Thanks!
I've tried following the GOplot github instructions to the T. I've successfully gotten the code to RUN, but its just not pulling information from my data files correctly.
