heatmap_generation function

Generate Heatmap

This function takes an inputted signature matrix as well as a list of genes and overlaps them. Then, if there is overlap, it prints a heatmap or barplot (depending on the number of overlapping genes). Then, for every cell-type, genes considered over-represented are saved in a list.

heatmap_generation(
  genesIn,
  comp,
  reference,
  cex = 0.8,
  rd_path = "",
  cellTypes = "ALL",
  pVal = 0.01,
  isPval = TRUE,
  isMax = FALSE,
  isBackground = FALSE,
  which_species = "human",
  toSave = FALSE,
  path = NULL
)

Arguments

• genesIn: A list of gene symbols (all caps) to have their cell type enrichment.
• comp: The name of the comparison.
• reference: Path to signature matrix or the signature matrix itself.
• cex: The size of the genes in the column label for the heatmap.
• rd_path: The directory to RData files -- if they are not in this directory, then the files will be downloaded.
• cellTypes: Colnames of the cell-types you will extract (passed to extract_genes_cell).
• pVal: The level of association a gene has within a cell type (passed to extract_genes_cell).
• isPval: If the signature matrix is raw p-value (T/F) -- TRUE not recommended
• isMax: If you are taking the single best CT marker (T/F) -- TRUE not recommended
• isBackground: If the heatmap is from the entire signature matrix or just the inputted gene list (T/F). isBackground == TRUE is used for internal.
• which_species: Species of gene symbols -- "human" or "mouse" .
• toSave: Allow scMappR to write files in the path directory (T/F).
• path: If toSave == TRUE, path to the directory where files will be saved.

Returns

List with the following elements: - genesIn: Vector of genes intersecting gene list and signature matrix.

• genesNoIn: Vector of inputted genes not in signature matrix.

• geneHeat: Signature matrix subsetted by inputted gene list

• preferences: Cell-markers mapping to cell-types.

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$POA_Rank_signature
Signature <- POA_Rank_signature
rowname <- get_gene_symbol(Signature)
rownames(Signature) <- rowname$rowname
genes <- rownames(Signature)[1:100]
heatmap_test <- heatmap_generation(genesIn = genes, "scMappR_test",
                                   reference = Signature, which_species = "mouse")