DORC J scatter plot — dorcJPlot • FigR

Function to visualize genes based on number of significant gene-peak correlations (per gene), used to define DORCs

Usage

dorcJPlot(
  dorcTab,
  cutoff = 7,
  labelTop = 25,
  returnGeneList = FALSE,
  cleanLabels = TRUE,
  labelSize = 4,
  ...
)

dorcTab: data.frame object containing significant peak-gene pairs using which DORC scores will be computed. Must be a filtered set returned from runGenePeakcorr. IMPORTANT: Make sure the exact same scATAC SE (peak set) was used when determining DORCs that is used here to get corresponding DORC peak counts
cutoff: numeric indicating cut-off to use for number of significant peaks per gene to call it a DORC. Default is 7 significant peaks per gene.
labelTop: numeric indicating the number of top genes to add labels for. Setting this to a very high number can lead to plot rendering difficulties (since labels get crowded).
returnGeneList: boolean indicating whether to also return the DORCs passing the provided filter. Default is FALSE (will just plot and nothing else)
cleanLabels: boolean indicating whether or not to try to have cleaner DORC gene labels. If TRUE, uses geom_text_repel, if FALSE, will use regular geom_text
labelSize: numeric indicating what to set label size to. Default is 4.
...: additional parameters passed to either geom_text_repel (if cleanLabels is set to TRUE) or geom_text. For example, set size to control font size, or segment.length or segment.color to control call-out segment length and color etc.

a ggplot object of the DORC J plot. If returnGeneList is set to TRUE, then also returns the vector of DORC genes passing the specified threshold

Vinay Kartha