plot_loadings_coordinatesV2: Plot Loadings Coordinates with Genomic Information
In eisascience/scCustFx: single-cell custom fxs Package

plot_loadings_coordinatesV2

R Documentation

Plot Loadings Coordinates with Genomic Information

Description

Generates a genomic coordinate plot of SDA component loadings. The function retrieves gene location data via biomaRt or uses a local file if provided and available, merges this with the loadings, and annotates the top positive and negative loading genes. Optionally, specific genes can be highlighted.

Usage

plot_loadings_coordinatesV2(
  SDARedDataLS,
  reduction,
  mart = NULL,
  genes = NULL,
  dimN,
  highlight_genes = NULL,
  TopNpos = 10,
  TopNneg = 10,
  data_set = "hsapiens_gene_ensembl",
  invertWeights = FALSE,
  includeUnMapped = TRUE,
  geneLocPath = NULL
)

Arguments

`SDARedDataLS`	A list containing SDA loadings.
`reduction`	Character or numeric value specifying which reduction to use from the loadings list.
`mart`	An optional biomaRt object; if `NULL`, it is initialized using `useMart` with `data_set`.
`genes`	An optional data frame of gene coordinates. If `NULL`, coordinates are retrieved via biomaRt.
`dimN`	Numeric value indicating the component (dimension) index to plot.
`highlight_genes`	Optional character vector of gene symbols to highlight in the plot.
`TopNpos`	Integer specifying the number of top positive loadings to annotate.
`TopNneg`	Integer specifying the number of top negative loadings to annotate.
`data_set`	Character string indicating the Ensembl dataset to use (e.g., `"hsapiens_gene_ensembl"`).
`invertWeights`	Logical. If `TRUE`, inverts the loading weights.
`includeUnMapped`	Logical. If `TRUE`, includes unmapped genes in the plot.
`geneLocPath`	Optional character string specifying the file path for pre-saved gene location data.