plotfigRNetwork: Plot FigR Network

In buenrostrolab/FigR: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data

Plot FigR Network

Description

Network visualization of TF-DORC associations based on the regulation scores inferred by FigR

Usage

plotfigRNetwork(
  figR.d,
  score.cut = 1,
  DORCs = NULL,
  TFs = NULL,
  weight.edges = FALSE,
  TFnodecol = "Tomato",
  DORCnodecol = "Sky Blue",
  posEdgecol = "Forest Green",
  negEdgecol = "Purple",
  labelSize = 13,
  showLegend = TRUE
)

Arguments

figR.d	data.frame of results returned by runFigRGRN)
score.cut	numeric specifying the absolute regulation score to threshold TF-DORC connections on. Default is 1
DORCs	character specifying valid DORC gene symbols to subset heatmap to. Default is NULL (no subsetting)
TFs	character specifying valid TF gene symbols to subset heatmap to. Default is NULL (no subsetting)
TFnodecol	character specifying valid color name to use for TF nodes. Default is Tomato
DORCnodecol	character specifying valid color name to use for DORC nodes. Default is Sky Blue
posEdgecol	character specifying valid color name to use for Activating edges between TFs and DORCs. Default is Forest Green
negEdgecol	character specifying valid color name to use for Repressive edges between TFs and DORCs. Default is Purple
labelSize	numeric specifying font size to use for all labels. Default is 13
showLegend	boolean indicating whether to show color legend. Default is TRUE
weight.edge	boolean specifying whether or not to weight edges by FigR regulation score. Default is FALSE

Value

a network plot of the resulting filtered TF-DORC associations

Author(s)

Vinay Kartha

buenrostrolab/FigR documentation built on Feb. 10, 2023, 11:26 a.m.