TOmicsVis (version 2.0.0)

dendro_plot: Dendrograms for multiple samples/groups clustering.

Description

Dendrograms for multiple samples/groups clustering.

Usage

dendro_plot(
  data,
  dist_method = "euclidean",
  hc_method = "ward.D2",
  tree_type = "rectangle",
  k_num = 5,
  palette = "npg",
  color_labels_by_k = TRUE,
  horiz = FALSE,
  label_size = 1,
  line_width = 1,
  rect = TRUE,
  rect_fill = TRUE,
  xlab = "Samples",
  ylab = "Height",
  ggTheme = "theme_light"
)

Value

Plot: dendrogram for multiple samples clustering.

Arguments

data

Dataframe: All genes 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: "ward.D2", options: "ward.D", "ward.D2", "single", "complete","average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

tree_type

Character: plot tree type. Default: "rectangle", options: "rectangle", "circular", "phylogenic".

k_num

Numeric: the number of groups for cutting the tree. Default: 3.

palette

Character: color palette used for the group. Default: "npg", options: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

color_labels_by_k

Logical: labels colored by group. Default: TRUE, options: TRUE or FALSE.

horiz

Logical: horizontal dendrogram. Default: FALSE, options: TRUE or FALSE.

label_size

Numeric: tree label size. Default: 0.8, min: 0.

line_width

Numeric: branches and rectangle line width. Default: 0.7, min: 0.

rect

Logical: add a rectangle around groups. Default: TRUE, options: TRUE or FALSE.

rect_fill

Logical: fill the rectangle. Default: TRUE, options: TRUE or FALSE.

xlab

Character: title of the xlab. Default: "".

ylab

Character: title of the ylab. Default: "Height".

ggTheme

Character: ggplot2 theme. Default: "theme_light", options: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void".

Author

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

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

# 3. Default parameters
dendro_plot(gene_expression)

# 4. Set palette = "aaas"
dendro_plot(gene_expression, palette = "aaas")

# 5. Set tree_type = "circular"
dendro_plot(gene_expression, tree_type = "circular")