tissue_scMappR_custom function

Gene List Visualization and Enrichment with Custom Signature Matrix

This function visualizes signature matrix, clusters subsetted genes, completes enrichment of individual cell-types and co-enrichment.

tissue_scMappR_custom(
  gene_list,
  signature_matrix,
  output_directory = "custom_test",
  toSave = FALSE,
  path = NULL,
  gene_cutoff = 1,
  is_pvalue = TRUE
)

Arguments

• gene_list: A list of gene symbols matching that of the signature_matrix. Any gene symbol is acceptable.
• signature_matrix: Pre-computed signature matrix with matching gene names.
• output_directory: Directory made containing output of functions.
• toSave: Allow scMappR to write files in the current directory (T/F).
• path: If toSave == TRUE, path to the directory where files will be saved.
• gene_cutoff: Value cut-off (generally rank := log10(Padj)) for a gene to be considered a marker.
• is_pvalue: If signature matrix is p-value before rank is applied (not recommended) (T/F).

Returns

List with the following elements: - background_heatmap: Data frame of the entire gene by cell-type signature matrix inputted.

• gene_list_heatmap: Data frame of inputted signature matrix subsetted by input genes.

• single_celltype_preferences: Data frame of enriched cell-types.

• group_celtype_preference: Data frame of groups of cell-types enriched by the same genes.

Details

This function is roughly the same as tissue_scMappR_internal, however now there is a custom signature matrix. It generates a heatmap of the signature matrix and your inputted gene list, as well as single cell-type and co-celltype enrichment.

Examples

# load in signature matrices
data(POA_example)
POA_generes <- POA_example$POA_generes
POA_OR_signature <- POA_example$POA_OR_signature
POA_Rank_signature <- POA_example$POA_Rank_signature
sig <- get_gene_symbol(POA_Rank_signature)
Signature <- POA_Rank_signature
rownames(Signature) <- sig$rowname
genes <- rownames(Signature)[1:60]
heatmap_test <- tissue_scMappR_custom(gene_list =  genes, signature_matrix = Signature,
                                      output_directory =  "scMappR_test", toSave = FALSE)