search

welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
380 stars 78 forks source link

plotgeneloadings, runGSEA, plotWordClouds error #275

Open Prathyusha-konda opened 1 year ago

Prathyusha-konda commented 1 year ago

Hi, I integrated scRNA datasets using the tutorial for "Integrating Seurat objects using LIGER" (https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/liger.html). I then converted the integrated seurat object to liger object using seuratToLiger before plotting GeneLoadings and running Wilcoxon test as per this tutorial (http://htmlpreview.github.io/?https://github.com/welch-lab/liger/blob/master/vignettes/Integrating_multi_scRNA_data.html). But I'm getting the following error with all downstream commands related to plotGeneLoadings, runGSEA, plotWordClouds, etc. Can you please let me know how to go about this?

gene_loadings <- plotGeneLoadings(ligerex3, do.spec.plot = FALSE, return.plots = TRUE) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': attempt to select less than one element in get1index