plot_volcano: Generating Volcano plot for differential gene expression...

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Function uses result gene list from differential expression analysis to prepare volcano plot.

Usage

plot_volcano(
  data,
  column_name_geme = NULL,
  column_name_p = "padj",
  column_name_fc = "log2FoldChange",
  title = "Volcano plot",
  p_value_threshold = 0.05,
  fc_threshold = log2(1.5),
  xlabel = "log fold change",
  ylabel = "-log10 p-value (adjusted)",
  color_down_reg = "red",
  color_up_reg = "darkgreen",
  color_not_reg = "darkgray"
)

Arguments

data	data.frame containing gene ID or Symbol (optional), p-value and logarithmized foldchange. Column names can be given in column_name_geme, column_name_p and column_name_fc, respectively.
column_name_geme	character with optional column name of gene names or symbols in data.
column_name_p	character with column name of p-values in data.
column_name_fc	character with column names of logarithmized fold changes in data.
title	character with title of volcano plot.
p_value_threshold	numeric significance threshold for p-value.
fc_threshold	numeric significance threshold for logarithmized fold changes.
xlabel	character with label for x-axis
ylabel	character with label for y-axis
color_down_reg	character with color name for indicating down regulated genes.
color_up_reg	character with color name for indicating up regulated genes.
color_not_reg	character with color name for indicating genes not differentially regulated.

Details

Input gene list is filtered for differentially expressed genes according to given significance thresholds for p-value and log foldchange. Significance thresholds are indicated as dashed lines in the plot. Up and down regulated genes can be colored accordingly. The counts of significantly differentially expressed genes is given in the upper plot margin.

Value

dataframe with filtered gene list. Volcano plot is generated as side effect.

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.