getQuantificationplot: get qunatification per run plot

In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description

This function can be used to generate a qunatification box plot per run

Usage

getQuantificationplot(
  data,
  fdr_threshold = 0.05,
  scores = "ipf_fdr",
  intensities = "ipf_Intensity",
  true_peptides = "ipf_TP",
  normalzied_relative_intensity = FALSE,
  keep.only.TP = TRUE,
  p.title = NULL,
  dataset = ""
)

Arguments

data	A data.table containing intensity information
fdr_threshold	A numeric vector to add fdr threshold lines to the plot. Default: fdr_threshold = 0.05
scores	A character vector of the data column name scores to filter data on
intensities	A character vector inficating the column to use for intentisty information
true_peptides	A character vector indicating the column header name containing true class labels
keep.only.TP	A logical value indicating to only show intensity information for true positive peptides
p.title	A character to label plot

Value

A a ggplot object

Author(s)

Justin Sing https://github.com/singjc

singjc/mstools documentation built on June 28, 2020, 8:10 p.m.