chord_plot: Chord plot for visualizing the relationships of pathways and...

In TOmicsVis: Transcriptome Visualization Process Scheme

Chord plot for visualizing the relationships of pathways and genes.

Description

Chord plot is used to visualize complex relationships between samples and genes, as well as between pathways and genes.

Usage

chord_plot(
  data,
  multi_colors = "VividColors",
  color_seed = 10,
  color_alpha = 0.3,
  link_visible = TRUE,
  link_dir = -1,
  link_type = "diffHeight",
  sector_scale = "Origin",
  width_circle = 3,
  dist_name = 3,
  label_dir = "Vertical",
  dist_label = 0.3,
  label_scale = 0.8
)

Arguments

data	Dataframe: Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~: Samples).
multi_colors	Character: color palette. Default: "VividColors", options: "VividColors", "RainbowColors".
color_seed	Numeric: rand seed for VividColors. Default: 10.
color_alpha	Numeric: color alpha. Default: 0.50, min: 0.00, max: 1.00.
link_visible	Logical: links visible. Default: TRUE, options: TRUE, FALSE.
link_dir	Numeric: links direction, use with link_type. Default: -1, options: -1, 0, 1, 2.
link_type	Character: links type, use with link_dir. Default: "diffHeight", options: "diffHeight", "arrows".
sector_scale	Character: sector scale method. Default: "Origin", options: "Origin", "Scale".
width_circle	Numeric: outside circle width. Default: 3.0, min: 0.0, max: 10.0.
dist_name	Numeric: the distance of name and circle. Default: 3.0, min: 0.0, max: 10.0.
label_dir	Character: label director. Default: "Vertical", options: "Horizontal", "Vertical".
dist_label	Numeric: the distance of label and circle. Default: 0.3, min: 0.0.
label_scale	Numeric: labels font size sclae. Default: 0.8, min: 0, max: NULL.

Value

Plot: chord plot is used to visualize complex relationships between samples and genes, as well as between pathways and genes.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_expression2)
head(gene_expression2)

# 3. Default parameters
chord_plot(gene_expression2[1:20,])

TOmicsVis documentation built on Aug. 29, 2023, 1:06 a.m.