plotLinks: plotLinks

In aertslab/ScoMAP: ScoMAP: Single-Cell Omics Mapping into spatial Axes using Pseudotemporal ordering

Description

Plot enhancer-to-gene links (To be enhanced)

Usage

plotLinks(
  RF_links = NULL,
  Cor_links = NULL,
  annot,
  txdb,
  org.db,
  gene,
  chr,
  start,
  end,
  cutoff = 0
)

Arguments

RF_links	Data frames list containing RF scores for each region in each gene as returned by enhancerToGene().
Cor_links	Data frames list containing correlation scores for each region in each gene as returned by enhancerToGene(). If both RF and correlation links are provided, the height of the links will represent the RF importance and the color whether the correlation is positive or negative. If only RF is provided, links will be colored black; and if only correlation links are provided the height of the lnk will indicate the absolute correlation value and the color whether it is positive or negative.
annot	Annotation data frame, as required by cicero (Pliner et al., 2019)
txdb	Txdb object matching with the genome assembly used for the analysis
org.db	Org.Db objet for the corresponding species
gene	Gene for which enhancer-to-gene links wants to be plotted
chr	Chromosome name of the genomic window that wants to be plotted
start	Start position of the genomic window that wants to be plotted
end	End position of the genomic window that wants to be plotted
cutoff	Value below which links will not be shown. Default: -1.

Examples

plotLinks(RF_links, dm6_annot, TxDb.Dmelanogaster.UCSC.dm6.ensGene, org.Dm.eg.db, gene='dac', 'chr2L', 16470000, 16490000)

aertslab/ScoMAP documentation built on Oct. 8, 2021, 1:15 a.m.