plot-isobaricnormRes: Plot isobaricnormRes object

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Plot isobaricnormRes object

Description

Creates box plots for an S3 object of type 'isobaricnormRes'

Usage

## S3 method for class 'isobaricnormRes'
plot(
  x,
  order = FALSE,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = NULL,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "none",
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Arguments

x	an object of type isobaricnormRes, created by normalize_isobaric with apply_norm = FALSE
order	logical value. If TRUE the samples will be ordered by the column of f_data containing the experiment/plate information.
interactive	logical value. If TRUE produces an interactive plot.
x_lab	character string specifying the x-axis label
y_lab	character string specifying the y-axis label
x_lab_size	integer value indicating the font size for the x-axis. The default is 11.
y_lab_size	integer value indicating the font size for the y-axis. The default is 11.
x_lab_angle	integer value indicating the angle of x-axis labels.
title_lab	character string specifying the plot title.
title_lab_size	integer value indicating the font size of the plot title. The default is 14.
legend_lab	character string specifying the legend title.
legend_position	character string specifying the position of the legend. Can be one of "right", "left", "top", "bottom", or "none". The default is "none".
bw_theme	logical value. If TRUE uses the ggplot2 black and white theme.
palette	character string indicating the name of the RColorBrewer palette to use. For a list of available options see the details section in RColorBrewer.
...	further arguments passed to or from other methods.

Value

ggplot2 plot object if interactive is FALSE, or plotly plot object if interactive is TRUE

Examples

library(pmartRdata)
myiso <- edata_transform(omicsData = isobaric_object, data_scale = "log2")
result <- normalize_isobaric(myiso,
  exp_cname = "Plex",
  apply_norm = FALSE,
  refpool_cname = "Virus",
  refpool_notation = "Pool"
)
plot(result)

pmartR/pmartRqc documentation built on March 4, 2024, 3:46 p.m.