gene_rank_plot {TOmicsVis}

Gene ranking dotplot for visualizing differentailly expressed genes.

Description

Gene ranking dotplot for visualizing differentailly expressed genes.

Usage

gene_rank_plot(
  data,
  log2fc = 1,
  palette = "Spectral",
  top_n = 10,
  genes_to_label = NULL,
  label_size = 5,
  base_size = 12,
  title = "Gene ranking dotplot",
  xlab = "Ranking of differentially expressed genes",
  ylab = "Log2FoldChange"
)

Arguments

data

Dataframe: All DEGs of paired comparison CT-vs-LT12 stats dataframe (1st-col: Genes, 2nd-col: log2FoldChange, 3rd-col: Pvalue, 4th-col: FDR).

log2fc

Numeric: log2(FoldChange) cutoff log2(2) = 1. Default: 1.0, min: 0.0, max: null.

palette

Character: color palette used for the point. Default: "spectral", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.

top_n

Numeric: number of top differentailly expressed genes. Default: 10, min: 0.

genes_to_label

Character: a vector of selected genes. Default: "NULL".

label_size

Numeric: gene label size. Default: 5, min: 0.

base_size

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

title

Character: main plot title. Default: "Gene ranking dotplot".

xlab

Character: title of the xlab. Default: "Ranking of differentially expressed genes".

ylab

Character: title of the ylab. Default: "Log2FoldChange".

Value

Plot: Gene ranking dotplot for visualizing differentailly expressed genes.

Author(s)

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

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

# 3. Default parameters
gene_rank_plot(degs_stats)

# 4. Set top_n = 5
gene_rank_plot(degs_stats, top_n = 5, palette = "PiYG")

# 5. Set genes_to_label = c("SELL","CCR7","KLRG1","IL7R")
gene_rank_plot(degs_stats, genes_to_label = c("SELL","CCR7","KLRG1","IL7R"), palette = "PuOr")