Comments (3)
@lucas-bishop Check how R is interpretting your "all_contig_anotations.csv" file, specifically the "productive" column. The formula for prep.vdj, F0039.R, includes a subset on line 22 that only keeps data if the value in the "productive" column is "True". However, when I investigated my "all_contig_anotations.csv" in RStudio, I found it was importing values in that columns as "true", "false" - the case of the first letter wasn't matching. So prep.vdj was subseting out all my data because technically R reads "True" as not equal to "true".
If that's your issue, this code worked for me
my.vdj$productive[my.vdj$productive == "true"] <- "True"
My.VDJ <- prep.vdj(my.vdj)
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@frazzette If I recall correctly I think I hacked together some code to coerce the "productive" column - similar to what you've done here. Thank you for the suggestion!
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Hi guys,
I am a bit busy but soon will look into this. But for now, I think it's important to know that the vdj analysis is mostly about plotting the clonotypes to spot them in UMAP, tSNE or KNetL. You can do this manually (outside of iCellR) too. Get the X and Y axes from the UMAP (in the umap.data slot) and plot the cells of interest in red and rest of the cells in gray for any clonotype. Hope this helps for now but once I have more time I will fix those functions and look into them.
Reza
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Related Issues (20)
- Error: cannot allocate vector of size 6288.3 Gb HOT 1
- convert seurat object to iCellR object HOT 3
- Ploting colonotypes HOT 4
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- Can I integrate data with iCellR? HOT 4
- Method for gene-gene correlations HOT 2
- How to normalize data with single condition? HOT 1
- Transform my iCellR object into seurat? HOT 1
- no plots available for ADT data when using ADT + HTO
- Seeking help to create different types of plots HOT 3
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