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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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SCEVAN output no consensus plot #53

Closed smdn-tt closed 1 year ago

smdn-tt commented 1 year ago

Greetings and thank you for this amazing package which has sped up my analyses significantly. I have run SCEVAN on a human tumour single nuclear dataset (10x), and the results are comparable with the WGS findings. However, I am in need of the consensus plots which look like typical ascat/battenberg CN profiles, but this file does not seem to have been created.

My code was as follows: results <- SCEVAN::pipelineCNA(count_mtx = rawcts, norm_cell = normcells, sample = "OS10", par_cores = 6, SUBCLONES = TRUE)

My output folder contains the following: list.files("./output/") [1] " OS10 vega_output" " OS10_SubcloneDiffAnalysis.RData" " OS10onlytumor vega_output"
[4] "OS10_Clonal_CN.seg" "OS10_CNAmtx.RData" "OS10_CNAmtxSubclones.RData"
[7] "OS10_count_mtx_annot.RData" "OS10_subclone1_CN.seg" "OS10_subclone2_CN.seg"
[10] "OS10_subclone3_CN.seg" "OS10-DEchr1-182393-6520061_subclones.png" "OS10CloneTree.png"
[13] "OS10heatmap_subclones.png" "OS10heatmap.png" "OS10OncoHeat.png"
[16] "OS10OncoHeat2.png" "OS10onlytumorheatmap.png" "OS10pathwayAnalysis_subclones1.png"
[19] "OS10pathwayAnalysis_subclones2.png" "OS10pathwayAnalysis_subclones3.png" "OS10tsne_CNA.png"
[22] "OS10tsne_scRNA.png"

I have SCEVAN 1.0.1 installed (running on R4.1.2)

A second question- the output file CNAmtx.Rdata does not have any rownames, how do I determine which chromosome location the scores represent for each cell? I am seeking to identify cells based on specific CN changes that I know are present from my WGS.

Your assistance is much appreciated!

Solange

AntonioDeFalco commented 1 year ago

Hi @smdn-tt, Thank you for your appreciation.

I am in need of the consensus plots which look like typical ascat/battenberg CN profiles, but this file does not seem to have been created.

Can you help me understand which type of plot you are referring to, with an example figure? I will be happy to help you generate it.

A second question- the output file CNAmtx.Rdata does not have any rownames, how do I determine which chromosome location the scores represent for each cell? I am seeking to identify cells based on specific CN changes that I know are present from my WGS.

You can find the row annotations in the SAMPLE_NAME_count_mtx_annot.RData file.

smdn-tt commented 1 year ago

Thank you for your speedy reply! The consensus figure is this one from the first tutorial. I am not certain if i need to include an additional option in my command?

image

And thank you for pointing to the row annotations.

Solange

AntonioDeFalco commented 1 year ago

Thank you for your speedy reply! The consensus figure is this one from the first tutorial. I am not certain if i need to include an additional option in my command? image

And thank you for pointing to the row annotations.

Solange

I corrected it in the last commit 802f8c1, now if you reinstall SCEVAN and re-run pipelineCNA you can get the consensus plot.

Let me know if everything is OK now. Regards.

smdn-tt commented 1 year ago

Works perfectly now, thank you!