8 Compare classifications

If two methods are used to classify cells (e.g. azimuth and hierarchical scPred), we can plot a contingeny table showing the concordance by cell type between the two methods.

Let’s create an output directory

mkdir step5_compare

And check the input arguments

singularity exec -B $PWD cell_classification.sif \  
  Rscript /compare.R --help

Usage: compare.R [options]


Options:
        --file=CHARACTER
                RDS object file name

        --xaxis=CHARACTER
                Column in metadata

        --yaxis=CHARACTER
                Column in metadata

        --sort=CHARACTER
                Sort labels in both axes to match cell type hierarchy?

        --out=CHARACTER
                Output file name [default= comp]

        --path=CHARACTER
                Output path to store results [default= .]

        -h, --help
                Show this help message and exit

Let’s assume we have a directory called step4_reduce a single .RDS file with cells classified with azimuth and hierarchical scPred. We can generate a heatmap showing the counts and proportion of cell type concordance between the two methods as well as a text file with the numeric results as follows:

singularity exec -B $PWD cell_classification.sif \ 
  Rscript /compare.R \
  --file step4_reduce/query.RDS \
  --out comparison \
  --path step5_compare

compare.R will output two heatmap plots corresponding to counts and proportion of cell type concordance between the two methods stored in the step5_compare directory.

7 Merge data