Support mtx(Matrix Market) file format as input

[CharleneZ95]

Dear CellPhoneDB Team, Since writing a large dataset to txt is a time-consuming task, see #138. I added a functionality to load .mtx (Matrix Market) file.

Example using .mtx as input:

cellphonedb method statistical_analysis test_meta.txt input_dir

Where input_dir is the directory containing the matrix.mtx, features.tsv, and barcodes.tsv files.

Using following code to generate input files in R:

library(Matrix)

expr_data <- as(as.matrix(expr_data), 'dgCMatrix')
features <- rownames(expr_data)
barcodes <- colnames(expr_data)

# output to file
writeLines(features, file = 'features.tsv')
writeLines(barcodes, file = 'barcodes.tsv')
writeMM(expr_data, file='matrix.mtx')

Where expr_data is the data matrix with row (genes) and column (cells) labels.

[dbrookeUAB]

The hero we deserve. This really needs to be implemented into the main branch. Text files are not sustainable.

[maxim-h]

Looks like the project is completely dead, which is a shame. Maybe someone will have the time to maintain an up-to-date fork in the future.

[stela2502]

Just a simple correction: The lines like writeLines(features, file = 'features.tsv') need to look like this: writeLines(features, con= 'features.tsv')

[prete]

Merged and fixed in #264