pmartR (version 2.4.6)

plot.cvFilt: Plot cvFilt Object

Description

For plotting an S3 object of type 'cvFilt'

Usage

# S3 method for 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,
  ...
)

Value

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

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.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
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)
}