gene_cluster_trend: Gene cluster trend plot for visualizing gene expression trend...

In TOmicsVis: Transcriptome Visualization Process Scheme

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
)

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.

Value

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

Author(s)

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")

TOmicsVis documentation built on Aug. 29, 2023, 1:06 a.m.