Comments (9)
Could you provide a bit more information please?
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I also have the error when run the function plotSpatialScatterpie( ).
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Hi @yutingdai1125 @wang0430
Could you please provide a reproducible example following these guidelines so that I can help you as efficiently as possible? Thank you!
from spotlight.
I found another error,
Error in plotImage(x = img) :
is.matrix(x) | is.character(x) | is.array(x) | is(x, "rastergrob") | .... is not TRUE
from spotlight.
Hi,
Can you return Seurat::Images(sample)
? Can you also try to pass img = GetImage(sample, mode = "grob"))
?
It is a bit hard to help you debug without further information,
Thank you,
Marc
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I don't think I'm the only one who encounters this problem. This happens when I use other public datasets, and I have been successful with these public datasets before. Have you modified your code recently? Need me to upload the data to you?
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I checked the source code and found that X (seurat object) was first converted into a matrix, and then x was required to be seurat, which caused me to keep making mistakes
from spotlight.
hi @wang0430
Can you try reinstalling SPOTlight from github?
devtools::install_github("https://github.com/MarcElosua/SPOTlight", ref = "main")
I have fixed that issue but haven't updated the code on Bioconductor, thank you for the heads up!
Marc
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hi @wang0430
Can you try reinstalling SPOTlight from github?
devtools::install_github("https://github.com/MarcElosua/SPOTlight", ref = "main")
I have fixed that issue but haven't updated the code on Bioconductor, thank you for the heads up!
Marc
hi,
I have recently encountered the same problem and have reinstalled as you suggested, but still no solution. What can I do please?
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Related Issues (20)
- In README.md the processed object can not find HOT 2
- Regarding the PBMC (GSE133549) dataset used in the method HOT 1
- scatter plot circles instead of sctter pie circles HOT 1
- residuals of the sum of squares doesn't work for Seurat object HOT 2
- Prepare for upcoming Seurat v5 release
- How to plot specific cell type proportions in the newest version of spotlight? HOT 1
- SPOTlight_1.0.0 on Bioconductor .zip cannot be downloaded
- dplyr::mutate() Error HOT 2
- downsample_se_obj HOT 1
- Questions about some details in paper HOT 2
- Fixed Matrix version incompatible with SeuratObject HOT 1
- Passing dataframe with NAs into plotCorrelationMatrix HOT 1
- Error from `.extract_counts()` when calling `SeuratObject::GetAssayData()` v5.0.1 HOT 1
- assay %in% SeuratObject::Assays(x) is not TRUE HOT 2
- How to annotate a spot as a type of cell HOT 1
- Error in .extract_coord(x = x, slice = slice, img = img) : !is.null(colnames(x)) is not TRUE HOT 1
- Scatterpie
- HELP! imgData is not equal to the spatialcoords
- trainNMF error HOT 7
- Subset Cells in ScatterPie HOT 1
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