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Plot gene expression or enrichment scores

Source: R/plotGenePathway.R
plotGenePathway.Rd

This function creates a plot for visualizing gene expression between partitions, either as a static plot or interactive with plotly.

Usage

plotGenePathway(
  K2res,
  feature,
  node,
  type = c("eMatDS", "eMat", "gMat"),
  use_plotly = TRUE,
  subsample = TRUE
)

Arguments

K2res

A K2 class object.

node

Character. A specific node identifier in K2res object.

type

Character. One of 'eMatDS' (default), 'eMat', or 'gMat'.

use_plotly

Logical. Whether to create a static plot, FALSE, or interactive plot, TRUE (default).

subsample

Logical. Whether to downsample the output object in order to save memory. This minimal impact on plot visual. Default is TRUE.

features

Character. Either a gene or gene set identifier.

Value

Either a ggplot or ggplotly object.

References

Reed ER, Monti S (2021). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Nucleic Acids Research. doi:10.1093/nar/gkab552 , https://pubmed.ncbi.nlm.nih.gov/34226941/.