cell_signatures: Cell_Signatures

In EDePasquale/Ericas_Functions: A Package of Erica's Most Used Functions for Processing Data Plus Random Utilities

Description

This function allows you to provide dimensionality coordinates and a gene by cell matrix to get cell signature overlays.

Usage

cell_signatures(
  coords,
  expression,
  signatures,
  file.path.prefix,
  cexsize = 1,
  type = "UMAP",
  subset = 30:45
)

Arguments

coords	Dataframe containing 2 columns, each for X and Y coordinates with rows as cells
expression	Dataframe of gene expression values, rows as genes and cells as columns
signatures	The signatures file, with each column as a seperate list of genes (signature) with headers
file.path.prefix	File path, including sample name, for plot to be saved as with the appropriate suffix. Example: "/Users/Documents/BPDCN123"
cexsize	The value that determines "cex" in the plot. Generated as part of the QC and Filter workflow but can be supplied independently. Default is 1
type	The type of plots to generate/the type of coordinates given. "UMAP" (default) and "tSNE" accepted
subset	Range of numeric values indicating which 16 plots to generate as the seperate "selected" plots. Default is 30:45 for the Griffin signatures

Examples

cell_signatures()

EDePasquale/Ericas_Functions documentation built on Dec. 17, 2021, 5:38 p.m.