heatmap_generation: Generate Heatmap
In scMappR: Single Cell Mapper

heatmap_generation

R Documentation

Generate Heatmap

Description

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.

Usage

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.

Value

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")

scMappR documentation built on July 9, 2023, 6:26 p.m.