Error in the graphfinder function

[GMaciag]

Thank you for the great work. I was trying to run tSpace on my dataset - 50 PCs of around 11000 cells. However, tSpace failed with error '"Error in -rem : invalid argument to unary operator"'. I debugged and traced the error to line 64 of the graphfinder function

tSpace/R/helper_functions.R

Line 98 in 0c85e13

temp <- temp[-rem,]

Turns out in my case 'rem' list is empty - it just contains 50 NULL objects. Because of this empty list the step mentioned above fails. The 'rem' object is created a few lines before in a parallel process I cannot debug further, so I'm not sure which line exactly is causing the problem.

Could you please assist me in solving this issue?

[hylasD]

Hi Grzegorz Could you please share with me your dataset and I can try to trace the error and investigate? Thx Denis

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On Mar 13, 2020, at 7:39 AM, Grzegorz Maciag ***@***.***> wrote:  Thank you for the great work. I was trying to run tSpace on my dataset - 50 PCs of around 11000 cells. However, tSpace failed with error "". I debugged and traced the error to line 64 of the graphfinder function https://github.com/hylasD/tSpace/blob/0c85e133ba4caf777f30cd8de1345f3252dc0c62/R/helper_functions.R#L98 Turns out in my case 'rem' list is empty - it just contains 50 NULL objects. Because of this empty list the step mentioned above fails. The 'rem' object is created a few lines before in a parallel process I cannot debug further, so I'm not sure which line exactly is causing the problem. Could you please assist me in solving this issue? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[GMaciag]

Hi Denis

I maybe should've mentioned that I'm preprocessing my data in scanpy before loading it into R. I checked and the error happens also with the pbmc3k dataset from scanpy's tutorial: https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/pbmc3k.html

After following the tutorial (at least until creating the PCA reduction) I save the PC representation of the data to a .mtx file with
mmwrite(target = "pbmc3k_tSPACE.mtx", a = sparse.csr_matrix(adata.obsm['X_pca'].T))
Then I load it into R, transform it to a dataframe and run tSpace with:

data <- Matrix::readMM(file = "./pbmc3k_tSPACE.mtx")
df <- as.data.frame(as.matrix(data))
ts <- tSpace(df = df, K = 20, D = 'pearson_correlation', graph = 5, 
             trajectories = 100, wp = 15, dr = 'pca', core_no = 40,
             ground_truth = T)

You can find the file with pbmc3k data I'm trying to run with tSpace here:
https://drive.google.com/open?id=1CdCr3gNPSQeDgA3XmS42iE1b9PE-LumI