search

kharchenkolab / pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
204 stars 47 forks source link

Error in hdea #137

Closed yojetsharma closed 2 years ago

yojetsharma commented 2 years ago

I am receiving the following error after the hdea step. I have loaded 10x outputs and ran the commands and faced no issues except at this step:

hdea <- r$getHierarchicalDiffExpressionAspects(type='PCA', clusterName='community', z.threshold=3) Using community clustering for PCA space

Error in if (nrow(x) < 1) return(NULL) : argument is of length zero

evanbiederstedt commented 2 years ago

@yojetsharma

I would far more details to diagnose this.

I suspect there's a problem upstream. As far as I know based on other examples, this function isn't buggy.

In any sense, this isn't needed to run Conos, which is what you're discussing in another thread.

yojetsharma commented 2 years ago

[114 [1] Z M highest fe Gene

<0 rows> (or 0-length row.names) $115 [1] Z M highest fe Gene <0 rows> (or 0-length row.names) $116 [1] Z M highest fe Gene <0 rows> (or 0-length row.names) $117 [1] Z M highest fe Gene <0 rows> (or 0-length row.names) $118 [1] Z M highest fe Gene <0 rows> (or 0-length row.names) Warning messages: 1: ggrepel: 35 unlabeled data points (too many overlaps). Consider increasing max.overlaps 2: ggrepel: 35 unlabeled data points (too many overlaps). Consider increasing max.overlaps de <- r$diffgenes$PCA[[1]][['3']] r$plotGeneHeatmap(genes=rownames(de)[1:15], groups=r$clusters$PCA[[1]]) de <- r$diffgenes$PCA[[1]][['2']] r$plotGeneHeatmap(genes=rownames(de)[1:15], groups=r$clusters$PCA[[1]]) Warning message: In r$plotGeneHeatmap(genes = rownames(de)[1:15], groups = r$clusters$PCA[[1]]) : The following specified genes were not found in the data: [MT-CO2 RPS14 RPS25 DYRK1A MYL6 RPL38 MAGI3 RPL19 TLE4 MT-ND2 LCORL NA NA NA NA], omitting Error in if (nrow(x) < 1) return(NULL) : argument is of length zero](url)

These were the warnings that I had received.