plot-cvFilt: Plot cvFilt Object

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

Plot cvFilt Object

Description

For plotting an S3 object of type 'cvFilt'

Usage

## S3 method for class 'cvFilt'
plot(
  x,
  cv_threshold = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 0,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  log_scale = TRUE,
  n_breaks = 15,
  n_bins = 30,
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Arguments

x	object of class cvFilt generated via cv_filter
cv_threshold	numeric value for cv threshold above which to remove the corresponding biomolecules
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. The default is NULL in which case the y-axis label will be the metric selected for the metric argument.
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. The default is 0.
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".
log_scale	logical value. Indicates whether to use a log2 transformed x-axis. The default is TRUE.
n_breaks	integer value specifying the number of breaks to use. You may get less breaks if rounding causes certain values to become non-unique. The default is 15.
n_bins	integer value specifying the number of bins to draw in the histogram. The default is 30.
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)
data(pep_object)
mypep <- group_designation(
  omicsData = pep_object,
  main_effects = "Phenotype"
)

cvfilt <- cv_filter(omicsData = mypep)

plot(cvfilt, cv_threshold = 20)
plot(cvfilt, cv_threshold = 10, log_scale = FALSE)

pmartR/pmartR documentation built on March 4, 2024, 8:32 a.m.