rcorces
commented
10 months ago Hi @erlun1! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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Problem: After running the code: enrichMotifs <- peakAnnoEnrichment( seMarker = markersPeaks, ArchRProj = proj, peakAnnotation = "Motif", cutOff = "FDR <= 0.01 & Log2FC >= 1.25"), I encountered an error when attempting to create a heatmap using: heatmapEM <- plotEnrichHeatmap(enrichMotifs, n = 10, transpose = FALSE). The error message received was "Error in dimnames<-.data.frame(tmp, value = value): invalid 'dimnames' given for data frame".
I used: R version 4.3.0, SummarizedExperiment version 1.30.2, ArchR version 1.0.2. Ultimately, I found that the issue lies in a specific line of code within plotEnrichHeatmap: "mat <- assays(seEnrich)[["mlog10Padj"]]". The problem with this line of code is that for a SummarizedExperiment object, it requires declaring "assays(enrichMotifs, withDimnames = FALSE)[['mlog10Padj']]" to correctly call the matrix. The default parameter for the assays function is "withDimnames = TRUE". This bug has existed since version 1.0.0 and was only recently discovered. I hope this information can be helpful to others facing the same issue.