Skip to content

Error for runScAnnotation #46

@ZhishenJ

Description

@ZhishenJ

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

Looking forward to your reply! Thanks a lot.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions