TSSPlot (pmbc, group.by='high.tss) + Nolegend

wenzhong4 commented 1 year ago

I run Vignettes "Human PBMCs"" in R4.3.1. The TSSPlot fails as following:

TSSPlot(pbmc, group.by = 'high.tss') + NoLegend() Error in TSSPlot(pbmc, group.by = "high.tss") : Position enrichment matrix not present in assay

timoast commented 1 year ago

Please run TSSEnrichment with fast=FALSE first

wenzhong4 commented 1 year ago

pbmc <- TSSEnrichment(object = pbmc, fast = FALSE) Extracting TSS positions Finding + strand cut sites [W::hts_idx_load3] The index file is older than the data file: atac_v1_pbmc_10k_fragments.tsv.gz.tbi Finding - strand cut sites [W::hts_idx_load3] The index file is older than the data file: atac_v1_pbmc_10k_fragments.tsv.gz.tbi Error in colnames<-(*tmp*, value = seq_len(length.out = region.width) - : attempt to set 'colnames' on an object with less than two dimensions

wenzhong4 commented 1 year ago

Hello I suggest you to rerun your code to see TSSenrichment () function?

I used R-4.3.1. I downloaded data and cope the code form Signac Analyzing PBMC scATAC-seq • Signac (stuartlab.org)https://stuartlab.org/signac/articles/pbmc_vignette.html [https://stuartlab.org/signac/logo.svg]https://stuartlab.org/signac/articles/pbmc_vignette.html Analyzing PBMC scATAC-seqhttps://stuartlab.org/signac/articles/pbmc_vignette.html Signac stuartlab.org

From: Tim Stuart @.> Sent: Wednesday, July 5, 2023 9:37 PM To: stuart-lab/signac @.> Cc: Liu, Wenzhong @.>; Author @.> Subject: Re: [stuart-lab/signac] TSSPlot (pmbc, group.by='high.tss) + Nolegend (Issue #1440)

Please run TSSEnrichment with fast=FALSE first

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stuart-lab / signac

TSSPlot (pmbc, group.by='high.tss) + Nolegend #1440