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AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
https://www.nature.com/articles/s41467-023-36790-9
GNU General Public License v3.0
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Error in annoteBandOncoHeat and Error in data.frame #46

Closed Crick0509 closed 8 months ago

Crick0509 commented 1 year ago

Thank you for your contribution to the bioinformation,I think SCEVAN is a gospel for many beginner.But I meet some problems when I run it.

the first problem is: [1] "found 3 subclones" percentage_cells_subsclone_1 percentage_cells_subsclone_2 percentage_cells_subsclone_3 0.5175202 0.2318059 0.2506739 [1] "Segmentation of subclone : 1" [1] "Segmentation of subclone : 2" [1] "Segmentation of subclone : 3" $_subclone1 Chr Start End Alteration segm.mean 15 2 111898479 119438520 2 0.180712 31 4 57030773 75941051 2 0.317688 63 8 81701334 102412841 2 0.177557 143 22 50185915 50628173 -2 -0.199268 59 7 140084746 158830253 -1 -0.122816

$_subclone2 Chr Start End Alteration segm.mean 26 6 30676389 33416453 -2 -0.261065 56 11 167784 8920084 -2 -0.139116 97 19 12796820 49526333 -2 -0.194117 64 12 110434825 120201235 -1 -0.102395 71 14 49893092 64533690 1 0.119032 86 17 5419641 8290092 -1 -0.122950

$_subclone3 Chr Start End Alteration segm.mean 6 1 151156664 153946696 -2 -0.183453 99 19 45488777 49658642 -2 -0.167078

$_shareSubclone Chr Start End Alteration segm.mean sh_sub Mean _share1 1 19303965 24673267 -2 -0.140455 1-2 0

**_Error in annoteBandOncoHeat(res_proc$count_mtx_annot, diffSubcl, res_subclones$n_subclones, :

(converted from warning) NAs introduced by coercion_**

#################################################################################################### but when I run another count_mtx,another problem occured: [1] "found 5 subclones" percentage_cells_subsclone_1 percentage_cells_subsclone_2 percentage_cells_subsclone_3 percentage_cells_subsclone_4 0.2212121 0.2252525 0.2868687 0.1686869 percentage_cells_subsclone_5 0.0979798 [1] "Segmentation of subclone : 1" [1] "Segmentation of subclone : 2" [1] "Segmentation of subclone : 3" [1] "Segmentation of subclone : 4" [1] "Segmentation of subclone : 5" Error in data.frame(..., check.names = FALSE) : (converted from warning)

this is my running code,and 'epithelial' is my seurat result: library(devtools) install_github("miccec/yaGST") install_github("AntonioDeFalco/SCEVAN")

library(SCEVAN) library(Seurat) suppressPackageStartupMessages(library(ggtree)) count_mtx = epithelial@assays$RNA@counts count_mtx[1:4,1:4] phe=epithelial@meta.data head(phe) colnames(phe)

count_mtx[1:4,1:4] results <- pipelineCNA(count_mtx)

I don't know how can I do for it and looking forward to your help!

AntonioDeFalco commented 1 year ago

but when I run another count_mtx,another problem occured: [1] "found 5 subclones" percentage_cells_subsclone_1 percentage_cells_subsclone_2 percentage_cells_subsclone_3 percentage_cells_subsclone_4 0.2212121 0.2252525 0.2868687 0.1686869 percentage_cells_subsclone_5 0.0979798 [1] "Segmentation of subclone : 1" [1] "Segmentation of subclone : 2" [1] "Segmentation of subclone : 3" [1] "Segmentation of subclone : 4" [1] "Segmentation of subclone : 5" Error in data.frame(..., check.names = FALSE) : (converted from warning)

Hello @Crick0509 regarding this error, have you tried reducing the number of cores used in parallel as suggested in previous issues? #43 #38

As for the other error, I am trying to understand what it could be due to.

Regards.

AntonioDeFalco commented 8 months ago

Duplicate of https://github.com/AntonioDeFalco/SCEVAN/issues/43 https://github.com/AntonioDeFalco/SCEVAN/issues/38