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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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sc3_plot_silhouette generate an empty plot #45

Closed yicheinchang closed 6 years ago

yicheinchang commented 6 years ago

Hi, I am applying SC3 on a big single cell RNAseq data set with about 3,000 cells and 27,000 genes.

Running sc3 itself is OK.

SC3 <- sc3(my_data, ks = 2:20, biology = TRUE, k_estimator = FALSE, pct_dropout_max = 95, gene_filter = TRUE, pct_dropout_min = 5)

However, I encounter several issues while generating the report. First, the sc3_plot_silhouette(SC3, k=5) returned me an empty plot image

The plot is still 'informative' since the silhouette width of each cluster and the average silhouette width are still visible. If sc3_plot_silhouette can not handle the large data set, is there an easy way to get rid of the blank silhouette?

Thanks in advance.

session info

wikiselev commented 6 years ago

Hi, thanks for reporting this! Are you working in RStudio? I have the same problem in RStudio, however, if I try to plot it to a file (using e.g. pdf function) or from a terminal, everything looks ok. Could you please confirm that you can reproduce this? Many thanks in advance. Vlad

yicheinchang commented 6 years ago

Confirm!! This plot function works in R console but not in RStudio and in RMarkdown. Thanks !!! @wikiselev