Plot commands

The plot subcommands create various quick visualizations to facilitate the analysis. Some of these plots are useful after performing association analyses to interpret the results.

pleiotropy

Generates a pleiotropy report of a given allele across multiple phenotypes.

Input dataset

You need to download the phewas results from Phewas HLA. Naturally, the file most include summary statistics of the requested allele.

graph_pathogens

Generates a graph useful to compare the proportions of binding and poorly binding peptides across different pathogens for a given HLA allele. The data is source from the IEDB database.

Additionally, a fisher’s exact test is performed to determine if the proportions of binding and poorly binding peptides are significantly different between the pathogens. If a resulting p-value is below 0.05 and the OR is greater than 1, it indicates that the provided HLA allele may not recognize peptides from one pathogen as effectively as other alleles of the same locus. This could suggest a potential susceptibility to infections caused by that pathogen.

Note

Please consider that not all alleles have sufficient data in the IEDB database to generate meaningful plots.

plot_ikmb_coverage

Produces a histogram with the coverage of each HLA gene from the ikmb HLA genotyping pipeline.