plotLinks: plotLinks

Description Usage Arguments Examples

View source: R/enhancerToGene.R

Description

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

Usage

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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

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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.