plot_loadings_coordinates: This function generates a plot of gene loadings along genomic...

In eisascience/scCustFx: single-cell custom fxs Package

This function generates a plot of gene loadings along genomic coordinates based on a Seurat object.

Description

This function generates a plot of gene loadings along genomic coordinates based on a Seurat object.

Usage

plot_loadings_coordinates(
  SDARedDataLS,
  reduction,
  mart = NULL,
  genes = NULL,
  dimN,
  highlight_genes = NULL,
  TopNpos = 10,
  TopNneg = 10,
  data_set = "hsapiens_gene_ensembl",
  invertWeights = F,
  includeUnMapped = T,
  geneLocPath = NULL
)

Arguments

SDARedDataLS	A list of SDA data
reduction	the name of the SDA run
dimN	the reduction
highlight_genes	A character vector of gene symbols to highlight in the plot (default is NULL).
TopNpos	The number of top positive loadings to display (default is 10).
TopNneg	The number of top negative loadings to display (default is 10).
data_set	passed to SDAtools:::get.location data_set default "hsapiens_gene_ensembl" can be mmulatta_gene_ensembl or mmusculus_gene_ensembl .. see ??useMart or do: mart = useMart('ensembl'), followed by listDatasets(mart).
invertWeights	to invert the loading weight i.e., -loadings
includeUnMapped	to include un mapped genes e.g. LOCs default = T

Value

A ggplot object representing the loadings along genomic coordinates.

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.