ggplot2_dotplot {ERSSA} | 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)

[Package ERSSA version 1.5.1 Index]