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MarcElosua / SPOTlight

Spatial Transcriptomics Capture Location Deconvolution
https://marcelosua.github.io/SPOTlight
GNU General Public License v3.0
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plotSpatialScatterpie #92

Closed wang0430 closed 1 year ago

wang0430 commented 1 year ago

hi， Error in plotSpatialScatterpie(sample, mat, cell_types = colnames(mat), : nrow(x) == nrow(y) is not TRUE nrow(sample) is gene nrow(mat) is celltype I have drawn pictures like this before without any problems, but this time I reported an error.

MarcElosua commented 1 year ago

Could you provide a bit more information please?

yutingdai1125 commented 1 year ago

I also have the error when run the function plotSpatialScatterpie( ).

MarcElosua commented 1 year ago

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!

wang0430 commented 1 year ago

I found another error,

Error in plotImage(x = img) : is.matrix(x) | is.character(x) | is.array(x) | is(x, "rastergrob") | .... is not TRUE 1681881495441

MarcElosua commented 1 year ago

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

wang0430 commented 1 year ago

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?

1681955097808 1681955110213 1681955136244

wang0430 commented 1 year ago

1681958096400 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

MarcElosua commented 1 year ago

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

biobirds9 commented 11 months ago

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?