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compassR reads tsv and csv files, whereas Compass default output name is reactions.txt which is tsv format.

@AlexKhodaverdian - can you please change it to csv to match the expected compassR format

@sequoia-tree - can you please add support for gz files? (readr already handles gz input, so just need to put it into the extension parsing logic)

I have run Compass with Recon2.2. however, there seem to be no recon2.2 extdata in compassR. How can I analyse my data then?

Maybe reword the messages below in a way that conveys they're info and part of normal operation rather than warnings that should be attended? e.g.: "Dropping 3019 reactions that are inconsistent for all cells", what do you think?

compass_data <- CompassData$new(compass_settings)
|======================| 100% 1566 MB
3019 reactions are inconsistent for all cells. They will be dropped.
204 reactions have too small a range of values. They will be dropped.204 reactions have too small a range of values. They will be dropped.

for example, right now the reactions.txt is read, processed, and only then fails (with no recovery to resume from) upon missing gene expression file. Similarly if gene expression file exists, but cell metadata does not.

To developers

Hello, thank you for developing such a great tool.

I finished the analysis using Compass and was doing the wilcox test

I keep getting this error message "Error in wilcox.test.default(group_A_values, group_B_values) :

not enough (non-missing) 'x' observations".

what's the problem??

thank you.

Finish the man page documentation.

1. Finish the inline documentation in all the R files. (Some things, you may be able to simply copy and paste from the wiki.) In io.R make it clear that every file should have a tsv or csv extension as appropriate, because we use the extension to determine which readr function to use!
2. Do roxygen2::roxygenize().

I.e., if user specifies a path for the cell_metadata_file arg, it overrides the search in the default directory specified by user_data_directory.

what do you think? As a user, I intuitively assumed this was the case and realized it wasn't only having gotten the error (which was after waiting minutes to load a large file)

Error message as:
<error/tibble_error_already_has_rownames>
.data must be a data frame without row names.
Backtrace:

1. CompassData$new(compass_settings)
2. tibble::column_to_rownames(., "metareaction_id")

Thank you so much!