autoGO (version 0.9.1)

volcanoplot: Volcano Plot

Description

Once the differential analysis has been performed, it is possible to visualize the volcano plots employing this function.

The volcano plot is generated by the employment of ggplot2, setting xlimit and ylimit based on the data. If there are genes with pvalue equal to infinity, those are forced to the maximum value of the pvalue. If 'my_comparison' paramater is not provided (default: NULL), the function will extract the name of the first subfolder inside "./results" and use it. The volcano plots are saved in the a subfolder for each comparison (Figure 1).

Usage

volcanoplot(
  DE_results,
  my_comparison = NULL,
  highlight_genes = NULL,
  log2FC_thresh = 0,
  padj_thresh = 0.05,
  del_csv = ",",
  outfolder = "./results"
)

Value

No return value. Files will be produced as part of normal execution.

Arguments

DE_results

DESeq2 results table. Accepts both a file (.tsv, .csv, tab-separated .txt) or a dataframe (see example below). Requires 'log2FoldChange' and 'padj' columns.

my_comparison

The comparison to plot (control_vs_treatment, a_vs_b, ...). If the user is employing the whole workflow use exactly the name of the comparison indicated in the comparison dataframe.

highlight_genes

A (optional) list of genes the user would like to highlight (label) in the volcano plot. It accepts a dataframe, a character vector or a path to a file in .txt format.

log2FC_thresh

Threshold value for log2(Fold Change) to highlight genes as differentially expressed (default = 0).

padj_thresh

Threshold value for adjusted p-value to highlight genes as significant (default = 0.05).

del_csv

Specify the delimiter of the .csv file (default = ","). This is because opening .csv files with Excel messes up the format and changes the delimiter to ";".

outfolder

The name to assign to the folder for output saving. (Default = "./results").

Examples

if (FALSE) {
filename <- "./results/H460.2D_vs_H460.3D.2p/DE_H460.2D_vs_H460.3D.2p_allres.tsv"
volcanoplot(
  DE_results = filename,
  my_comparison = "H460.2D_vs_H460.3D.2p",
  log2FC_thresh = 0,
  padj_thresh = 0.05,
  highlight_genes = NULL,
  del_csv = ",",
  outfolder = "./results"
)
}