circos_heatmap {TOmicsVis}

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,])