TOmicsVis (version 2.0.0)

gene_cluster_trend: Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Description

Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Usage

gene_cluster_trend(
  data,
  thres = 0.25,
  min_std = 0.2,
  palette = "PiYG",
  cluster_num = 4
)

Value

Plot: Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Arguments

data

Dataframe: Shared DEGs of all paired comparisons in all groups expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~n-1-col: Groups, n-col: Pathways).

thres

Number: set the threshold for excluding genes. Default: 0.25.

min_std

Number: set the threshold for minimum standard deviation. Default: 0.2.

palette

Character: set the color palette to be used for plotting. Default: "PiYG", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.

cluster_num

Number: set the number of clusters. Default: 4.

Author

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset gene_cluster_data
data(gene_expression3)
head(gene_expression3)

# 3. Default parameters
gene_cluster_trend(gene_expression3[,-7])

# 4. Set palette = "RdBu"
gene_cluster_trend(gene_expression3[,-7], palette = "RdBu")

# 5. Set cluster_num = 6
gene_cluster_trend(gene_expression3[,-7], cluster_num = 6, palette = "Spectral")