volcano_plot: Volcano plot
In lisaschneider0509/lipidomeComparisonR:

'volcano_plot' prints a volcano plot using a data frame containing p-values and foldchanges

volcano_plot(
  volcano_df,
  foldchange_col,
  significance_col,
  significance = 0.05,
  foldchange = 1,
  title = "Volcano plot",
  x_lab = "log2Foldchange",
  y_lab = "-log10(p-value)",
  labels = TRUE,
  out_path = "none"
)

`volcano_df`	data frame.
`foldchange_col`	vector. Column of volcano_df containing the foldchange values. Format: volcano_df$foldchange_col
`significance_col`	vector. Column of volcano_df containing the p-values. Format: volcano_df$significance_col
`significance`	numeric. Value for the significance threshold. Default = 0.05.
`foldchange`	numeric. Vaue for the foldchange threshold. Default = #todo
`title`	string. Main title. Default = "Volcano plot"
`x_lab`	string. x-axix title. Default = "log2Fold"
`y_lab`	string. y-axis title- Default = "-log10(p-value)"
`labels`	logical. Should the points over the threshold be labelled. Options: TRUE (default), FALSE
`out_path`	string. Path to save plot to png. If out_path is empty, the plot is printed to the device. If "none", the plot is either printed or saved to a variabe.

This function takes a data frame with columns for p-values and (log2)foldchanges and returns a dotplot resembelling a volcano plot. It uses the given significance and foldchange threshods to mark significantly up- and down-regulated elements by color and by displaying threshold lines.

lisaschneider0509/lipidomeComparisonR documentation built on Aug. 12, 2020, 12:52 a.m.