assess_rank_bias {clustifyr} | R Documentation |
Find rank bias
assess_rank_bias( avg_mat, ref_mat, query_genes = NULL, res, organism, plot_name = NULL )
avg_mat |
average expression matrix |
ref_mat |
reference expression matrix |
query_genes |
original vector of genes used to clustify |
res |
dataframe of idents, such as output of cor_to_call |
organism |
for GO term analysis, organism name: human - 'hsapiens', mouse - 'mmusculus' |
plot_name |
name for saved pdf, if NULL then no file is written (default) |
pdf of ggplot object
## Not run: avg2 <- average_clusters( pbmc_matrix_small, pbmc_meta$seurat_clusters ) res <- clustify( input = pbmc_matrix_small, metadata = pbmc_meta, ref_mat = cbmc_ref, query_genes = pbmc_vargenes, cluster_col = "seurat_clusters" ) call1 <- cor_to_call( res, metadata = pbmc_meta, cluster_col = "seurat_clusters", collapse_to_cluster = FALSE, threshold = 0.8 ) res_rank <- assess_rank_bias( avg2, cbmc_ref, res = call1 ) ## End(Not run)