heatmap_cluster {TOmicsVis}

Heatmap cluster for visualizing clustered gene expression data.

Description

Heatmap cluster for visualizing clustered gene expression data.

Usage

heatmap_cluster(
  data,
  dist_method = "euclidean",
  hc_method = "average",
  k_num = 5,
  show_rownames = FALSE,
  palette = "RdBu",
  cluster_pal = "Set1",
  border_color = "#ffffff",
  angle_col = 45,
  label_size = 10,
  base_size = 12,
  line_color = "#0000cd",
  line_alpha = 0.2,
  summary_color = "#0000cd",
  summary_alpha = 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).

dist_method

Character: distance measure method. Default: "euclidean", options: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski".

hc_method

Character: hierarchical clustering method. Default: "average", options: "ward.D", "ward.D2", "single", "complete","average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

k_num

Numeric: the number of groups for cutting the tree. Default: 5.

show_rownames

Logical: boolean specifying if column names are be shown. Default: FALSE, options: TRUE or FALSE.

palette

Character: color palette used in heatmap. Default: "RdBu", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.

cluster_pal

Character: color palette used for the cluster. Default: "Set1", options: 'Set1', 'Set2', 'Set3', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2'.

border_color

Character: cell border color (color name or hex value). Default: "#ffffff".

angle_col

Numeric: angle of the column labels. Default: 45.

label_size

Numeric: fontsize for the plot. Default: 10, min: 0.

base_size

Numeric: base font size. Default: 12, min: 0.

line_color

Character: trend lines color. Default: "#0000cd".

line_alpha

Numeric: trend lines alpha. Default: 0.20, min: 0.00, max: 1.00.

summary_color

Charater: summary line color. Default: "#0000cd".

summary_alpha

Numeric: summary line alpha. Default: 0.80, min: 0.00, max: 1.00.

Value

Plot: Heatmap cluster for visualizing clustered gene expression data.

Author(s)

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

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

# 3. Default parameters
heatmap_cluster(gene_expression2)

# 4. Set palette = "PuOr"
heatmap_cluster(gene_expression2, palette = "PuOr")

# 5. Set line_color = "#ff0000", summary_color = "#ff0000"
heatmap_cluster(gene_expression2, line_color = "#ff0000", summary_color = "#ff0000")