circos_heatmap: Circos heatmap plot for visualizing gene expressing in...

In TOmicsVis: Transcriptome Visualization Process Scheme

Circos heatmap plot for visualizing gene expressing in multiple samples.

Description

Circos heatmap plot for visualizing gene expressing in multiple samples.

Usage

circos_heatmap(
  data,
  low_color = "#0000ff",
  mid_color = "#ffffff",
  high_color = "#ff0000",
  gap_size = 25,
  cluster_run = TRUE,
  cluster_method = "complete",
  distance_method = "euclidean",
  dend_show = "inside",
  dend_height = 0.2,
  track_height = 0.3,
  rowname_show = "outside",
  rowname_size = 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).
low_color	Character: min value color (color name or hex value). Default: "#0000ff".
mid_color	Character: middle value color (color name or hex value). Default: "#ffffff".
high_color	Character: high value color (color name or hex value). Default: "#ff0000".
gap_size	Numeric: heatmap gap size. Default: 25, min: 0.
cluster_run	Logical: running cluster algorithm. Default: TRUE, options: TRUE, FALSE.
cluster_method	Character: cluster methods. Default: "complete", options: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid".
distance_method	Character: distance methods. Default: "euclidean", options: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski".
dend_show	Character: control dendgram display and position. Default: "inside", options: "none", "outside", "inside".
dend_height	Numeric: dendgram height. Default: 0.20, min: 0.00, max: 0.50.
track_height	Numeric: heatmap track height. Default: 0.30, min: 0.00, max: 0.50.
rowname_show	Character: control rownames display and position. Hind first rowname by running rownames(data). Default: "outside", options: "none", "outside", "inside".
rowname_size	Numeric: rowname font size. Default: 0.80, min: 0.10, max: 10.00.

Value

Plot: circos heatmap plot for visualizing gene expressing in multiple samples.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

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

# 3. Default parameters
circos_heatmap(gene_expression2[1:50,])

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