Plot proteomicsFilt Object — plot.proteomicsFilt • pmartR

For plotting an S3 object of type 'proteomicsFilt':

# S3 method for class 'proteomicsFilt'
plot(
  x,
  plot_type = "num_peps",
  min_num_peps = NULL,
  interactive = FALSE,
  x_lab_pep = NULL,
  x_lab_pro = NULL,
  y_lab_pep = NULL,
  y_lab_pro = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 0,
  title_lab_pep = NULL,
  title_lab_pro = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  text_size = 3,
  bar_width = 0.8,
  bw_theme = TRUE,
  palette = NULL,
  display_count = TRUE,
  ...
)

Arguments

x: object of class proteomicsFilt, which is a list with two elements. The first element is a data frame of counts for each unique peptide. The second element is a data frame with the counts for the number of peptides that map to each unique protein.
plot_type: character string specifying the type of plot to be displayed. The available options are "num_peps" or "redundancy". If "num_peps" the plot is displayed that shows the counts of proteins that have a specific number of peptides mapping to them. If "redundancy" the plot showing the counts of peptides that map to a specific number of proteins is displayed.
min_num_peps: an optional integer value between 1 and the maximum number of peptides that map to a protein in the data. The value specifies the minimum number of peptides that must map to a protein. Any protein with less than min_num_peps mapping to it will be returned as a protein that should be filtered. Default value is NULL.
interactive: logical value. If TRUE produces an interactive plot.
x_lab_pep: character string used for the x-axis label for the num_peps plot. The default is NULL in which case the default x-axis label will be used.
x_lab_pro: character string used for the x-axis label for the redundancy plot. The default is NULL in which case the default x-axis label will be used.
y_lab_pep: character string used for the y-axis label for the num_peps plot. The default is NULL in which case the default y-axis label will be used.
y_lab_pro: character string used for the y-axis label for the redundancy plot. The default is NULL in which case the default y-axis label will be used.
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_pep: character string specifying the num_peps plot title. The default is NULL in which case the default title will be used.
title_lab_pro: character string specifying the redundancy plot title. The default is NULL in which case the default title will be used.
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".
text_size: An integer specifying the size of the text (number of peptides or proteins depending on the plot) within the bar plot. The default is 3.
bar_width: An integer indicating the width of the bars in the bar plot. The default is 0.8.
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.
display_count: logical value. Indicates whether the peptide or protein counts will be displayed on the bar plot. The default is TRUE.
...: 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)
my_filter <- proteomics_filter(omicsData = pep_object)
plot(my_filter, min_num_peps = 3)
plot(my_filter, plot_type = "redundancy")