Closed yicheinchang closed 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
Confirm!! This plot function works in R console but not in RStudio and in RMarkdown. Thanks !!! @wikiselev
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.
However, I encounter several issues while generating the report. First, the![image](https://user-images.githubusercontent.com/5447168/32451628-4ae4e446-c2e5-11e7-854a-f4b8eae47087.png)
sc3_plot_silhouette(SC3, k=5)
returned me an empty plotThe 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