Generate a Volcano plot from the table of linear regression models

Given a table generated with the function gentab_lm_long, it create a Volcano plot.

Usage

Volcano_lm(
  tab,
  ind_main,
  x_values = "variation_perc",
  y_values = "negative_log10fdr",
  dep_cat = FALSE,
  category = NULL,
  cut_off_names = -log10(1e-04),
  line1 = TRUE,
  line1_position = -log10(0.05),
  line2 = TRUE,
  line2_position = -log10(1e-04)
)

Arguments

tab: a dataframe created with the function gentab_lm_long.
ind_main: character of length 1. The independent variable to visualise in the Volcano plot. Important: for factor variables, it must me the name of the factor and the name of the level combined without space. e.g.: if the variable is "Sex" and the level is "Female", you must pass here "SexFemale".
x_values: character of length 1. The name of the column in tab containing the value to plot as x.
y_values: character of length 1. The name of the column in tab containing the value to plot as y.
dep_cat: logical. Do you want to color the dependent variable based on a certain category?
category: character of length 1. If dep_cat is TRUE, pass here the name of the column in tab that contains the categorisation.
cut_off_names: numerical of length 1. Names of dependent variables will be shown only if above this cut-off.
line1: logical. Do you want to show a horizontal dotted line?
line1_position: numerical of length 1. If line1 is TRUE, pass here the value of the dotted line.
line2: logical. Do you want to show a second horizontal dotted line?
line2_position: numerical of length 1. If line2 is TRUE, pass here the value of the second dotted line.

Value

a ggplot object, with the Volcano plot.