ggplot2_dotplot: Plot number of DE genes
In zshao1/ERSSA: Empirical RNA-seq Sample Size Analysis

ggplot2_dotplot

R Documentation

Plot number of DE genes

Description

ggplot2_dotplot function plots the number of differentially expressed (DE) genes in each test.

Usage

ggplot2_dotplot(deg = NULL, path = ".", save_plot = TRUE)

Arguments

`deg`	The list of DE genes generated by one of ERSSA::DE_*.R scripts.
`path`	Path to which the plot will be saved. Default to current working directory.
`save_plot`	Boolean. Whether to save plot to drive. Default to TRUE.

Details

The number of DE genes are plotted as dots grouped by the associated replicate level. At each replicate level, a boxplot is drawn to mainly show the first and third quartiles as well as the median. Additionally, A red line is drawn representing the mean at each replicate level. A horizontal dashed blue line represents the number of DE genes found with all samples.

Value

A list is returned containing:

gg_object the ggplot2 object, which can then be further customized.
deg_dataframe the tidy table version of DEG numbers for plotting.
full_num_DEG The number of DE genes with all samples included.

Author(s)

Zixuan Shao, Zixuanshao.zach@gmail.com

References

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2009.

Examples

# load edgeR deg object generated by erssa_edger using example dataset
# example dataset containing 1000 genes, 4 replicates and 5 comb. per rep.
# level
data(deg.partial, package = "ERSSA")

gg_dot = ggplot2_dotplot(deg.partial)

zshao1/ERSSA documentation built on July 19, 2023, 9:20 p.m.