Thanks a lot for creating a fantastic tool. However, there's a weird error when running 'runScAnnotation'.
There occurs an error during 'Seurat plotting and saving'. Seems like there could be something wrong with the parameter of 'geom_point'. The source code has been checked and the weird '#85f44' was not found. In the result files, the dimplots for cell markers are successfully plotted, but the folder 'report-figures' is empty.
anno.results <- runScAnnotation(
dataPath = dataPath,
statPath = statPath,
savePath = savePath,
authorName = authorName,
sampleName = sampleName,
geneSet.method = "average"
)
[2024-09-29 11:25:09.402259] START: RUN scAnnotation
Warning in 'prepareSeurat': Cannot find the raw data, and use the filtered data instead.
[2024-09-29 11:25:09.404979] -----: data preparation
[2024-09-29 11:29:18.428387] -----: Seurat object creation
[2024-09-29 11:29:46.074507] -----: highly variable genes
[2024-09-29 11:30:34.868678] -----: data scaling
[2024-09-29 11:36:51.383202] -----: PCA
[2024-09-29 11:38:51.005444] -----: clustering
[2024-09-29 11:41:02.985076] -----: tSNE
[2024-09-29 11:59:11.997376] -----: UMAP
[2024-09-29 12:03:12.801555] -----: differential expression analysis
[2024-09-29 15:39:57.133398] -----: Seurat plotting and saving
When using repel, set xnudge and ynudge to 0 for optimal results
Error in geom_point():
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error:
! Malformed colour string #85f44. Must contain either 6 or 8 hex values
Run rlang::last_trace() to see where the error occurred.
Warning message:
Transformation introduced infinite values in continuous x-axis
Thanks a lot for creating a fantastic tool. However, there's a weird error when running 'runScAnnotation'. There occurs an error during 'Seurat plotting and saving'. Seems like there could be something wrong with the parameter of 'geom_point'. The source code has been checked and the weird '#85f44' was not found. In the result files, the dimplots for cell markers are successfully plotted, but the folder 'report-figures' is empty.
Looking forward to your reply! Thanks a lot.