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CellDimPlot doesn't work #260

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Gbourm opened this issue Sep 28, 2024 · 3 comments
Open

CellDimPlot doesn't work #260

Gbourm opened this issue Sep 28, 2024 · 3 comments

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@Gbourm
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Gbourm commented Sep 28, 2024

Hello,
I have a problem when making the graphs, there is something wrong with the color so no graph is generated. Below are the warning message.

CellDimPlot(

  • srt = Exp1, group.by = "seurat_clusters", stat.by = "Phase",
  • reduction = "UMAP", theme_use = "theme_blank"
  • )
    Warning messages:
    1: No shared levels found between names(values) of the manual scale and the data's fill values.
    2: No shared levels found between names(values) of the manual scale and the data's fill values.
    3: No shared levels found between names(values) of the manual scale and the data's fill values.
    4: No shared levels found between names(values) of the manual scale and the data's fill values.

Could you help me solve this? I tried to look for solutions but couldn't find anything.
Thanks a lot,
Best
@Gbourm
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Gbourm commented Sep 29, 2024

More specifically, these warnings happen in all graphs, but the only ones that do not generate a graph are when "stat.by = "Phase" is used.
I am still trying to find out why, any help would be welcomed.

@Gbourm
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Gbourm commented Oct 2, 2024

Same happens with the trajectory inference
pancreas_sub <- RunSlingshot(srt = pancreas_sub, group.by = "SubCellType", reduction = "UMAP")

Warning messages:
1: No shared levels found between names(values) of the manual scale and the data's fill values.
2: No shared levels found between names(values) of the manual scale and the data's fill values.

@scb-jjames
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Did you solve this? I'm facing the same issue.

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@Gbourm @scb-jjames