plot_loadings_coordinates.seurat: 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.seurat(
  SerObj,
  reduction = "pca",
  redLab = "PC",
  loadingsLS = NULL,
  highlight_genes = NULL,
  TopNpos = 10,
  TopNneg = 10,
  data_set = "hsapiens_gene_ensembl",
  dimN = 1,
  invertWeights = F,
  includeUnMapped = T,
  geneLocPath = NULL
)

Arguments

SerObj	A Seurat object.
reduction	The dimensionality reduction method used in Seurat (default is "pca").
loadingsLS	Give a list of loadings to use instead of Seurat object SDA 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 .. see ??useMart or do: mart = useMart('ensembl'), followed by listDatasets(mart).
dimN	the reduction dim default = 1
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.