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

Description Usage Arguments Details Value Author(s)

Description

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

Usage

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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.