GOChord: Displays the relationship between genes and terms.

Description Usage Arguments

View source: R/internal.R

Description

The GOChord function generates a circularly composited overview of selected/specific genes and their assigned processes or terms. More generally, it joins genes and processes via ribbons in an intersection-like graph.

Usage

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GOChord(data, title, space, gene.order, gene.size, gene.space, nlfc = 1,
  lfc.col, lfc.min, lfc.max, ribbon.col, border.size, process.label, limit)

Arguments

data

The matrix represents the binary relation (1= is related to, 0= is not related to) between a set of genes (rows) and processes (columns); a column for the logFC of the genes is optional

title

The title (on top) of the plot

space

The space between the chord segments of the plot

gene.order

A character vector defining the order of the displayed gene labels

gene.size

The size of the gene labels

gene.space

The space between the gene labels and the segement of the logFC

nlfc

Defines the number of logFC columns (default=1)

lfc.col

The fill color for the logFC specified in the following form: c(color for low values, color for the mid point, color for the high values)

lfc.min

Specifies the minimium value of the logFC scale (default = -3)

lfc.max

Specifies the maximum value of the logFC scale (default = 3)

ribbon.col

The background color of the ribbons

border.size

Defines the size of the ribbon borders

process.label

The size of the legend entries

limit

A vector with two cutoff values (default= c(0,0)).


StarBioTrek documentation built on Nov. 8, 2020, 8:02 p.m.