plot_abundance_vs_percent

Plot relative protein abundance as a function of rank by abundance

Description

Plot relative protein abundance as a function of rank by abundance

Usage

plot_abundance_vs_percent(
  percInfo,
  cfg_config,
  top_N = 10,
  factors = TRUE,
  colors = c(`^REV_` = "red", `^CON_` = "orange"),
  columnAb = "abundance_percent",
  group = "BB",
  alpha = 1,
  highlight_alpha = 1,
  logY = TRUE
)

Arguments

percInfo data frame with percentage abundance info

cfg_config AnalysisConfiguration object

top_N number of top proteins to label

factors if TRUE facet by factors

colors named vector of colors for special proteins

columnAb column name for abundance values

group crosstalk group identifier

alpha point transparency for regular (black) proteins

highlight_alpha point transparency for highlighted (coloured) proteins

logY if TRUE use log10 y-axis

Value

ggplot2

Examples

library("prolfquapp")


library(prolfqua)
istar <- prolfqua::prolfqua_data('data_ionstar')$filtered()
data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100))
lfqdata <- prolfqua::LFQData$new(data, istar$config)
sr <- lfqdata$get_Summariser()
undebug(plot_abundance_vs_percent)
plot_abundance_vs_percent(sr$percentage_abundance(),
 lfqdata$get_config(),
 top_N = 6, factors = FALSE, logY = TRUE)

pd <- plot_abundance_vs_percent(
  sr$percentage_abundance(),
  lfqdata$get_config(), top_N = NULL, factors = FALSE)
plot_abundance_vs_percent(
  sr$percentage_abundance(),
  lfqdata$get_config(), top_N = 4, factors = TRUE)

plot_abundance_vs_percent(
  sr$percentage_abundance(),
  lfqdata$get_config(), top_N = NULL, factors = TRUE)