plot_volcano_basic: Plot basic volcano

In lagelab/Genoppi: genoppi

Plot basic volcano

Description

Plot protein-level data in a basic volcano plot. Can be chained with plot_overlay to produce overlays.

Usage

plot_volcano_basic(
  df,
  col_significant = "#41AB5D",
  col_other = "grey",
  sig_text = "(significant)",
  insig_text = "(not significant)",
  size_gg = 3,
  shape = 21,
  stroke = 0.2,
  col_border = NULL,
  plot_segments = F
)

Arguments

df	data.frame with at least columns gene, logFC, pvalue and significant.
col_significant	string. The color of significant proteins/genes.
col_other	string. The color of non-significant proteins/genes.
sig_text	string. Text for significant interactor to be displayed in legend.
insig_text	string. Text for non-significant interactors to be displayed in legend.
size_gg	numeric. The size of the points.
shape	integer. The shape of the points. Default to 21 (circles).
stroke	numeric. Stroke width.
col_border	string. A color for the outline of points.
plot_segments	boolean. Plot volcano plot axis segments, i.e. two lines with x and y axis intercept.

Examples

## Not run: 
p = example_data %>% 
calc_mod_ttest() %>%
  id_significant_proteins(fdr_cutoff = 0.1) %>%
  plot_volcano_basic() %>%
  plot_overlay(as.bait('BCL2')) 
p + ggtitle('Example volcano plot') + theme_classic()


## End(Not run)

lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.