heatmap_group {TOmicsVis}

Heatmap group for visualizing grouped gene expression data.

Description

Heatmap group for visualizing grouped gene expression data.

Usage

heatmap_group(
  sample_gene,
  group_sample,
  scale_data = "row",
  clust_method = "complete",
  border_show = TRUE,
  border_color = "#ffffff",
  value_show = TRUE,
  value_decimal = 2,
  value_size = 5,
  axis_size = 8,
  cell_height = 10,
  low_color = "#00880055",
  mid_color = "#ffffff",
  high_color = "#ff000055",
  na_color = "#ff8800",
  x_angle = 45
)

Arguments

sample_gene

Dataframe: Shared degs of all paired comparisons in all samples expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~: Samples).

group_sample

Dataframe: Samples and groups for gene expression (1st-col: Samples, 2nd-col: Groups).

scale_data

Character: scale data. Default: "row", options: "row", "column", "none".

clust_method

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

border_show

Logical: show border. Default: TRUE, options: TRUE, FALSE.

border_color

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

value_show

Logical: show value in cell. Default: TRUE, options: TRUE, FALSE.

value_decimal

Numeric: cell value decimal. Default: 2, min: 0, max: 5.

value_size

Numeric: cell value font size. Default: 5, min: 0, max: NULL.

axis_size

Numeric: axis title font size. Default: 8, min: 0, max: NULL.

cell_height

Numeric: cell height for value size and axis size. Default: 10.

low_color

Character: min value color (color value or hex value with alpha). Default: "#00880055".

mid_color

Character: min value color (color value or hex value with alpha). Default: "#ffffff".

high_color

Character: min value color (color value or hex value with alpha). Default: "#ff000055".

na_color

Character: min value color (color value or hex value with alpha). Default: "#ff8800".

x_angle

Numeric: x axis text angle. Default: 45, min: 0, max: 360.

Value

Plot: Heatmap group for visualizing grouped gene expression data.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

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

data(samples_groups)
head(samples_groups)

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

# 4. Set scale_data = "column"
heatmap_group(gene_expression2[1:50,], samples_groups, scale_data = "column")

# 5. Set value_show = FALSE
heatmap_group(gene_expression2[1:50,], samples_groups, value_show = FALSE)

# 6. Set low_color = "#00008888"
heatmap_group(gene_expression2[1:50,], samples_groups, low_color = "#00008888")