plot.proteomicsFilt {pmartR}

Plot proteomicsFilt Object

Description

For plotting an S3 object of type 'proteomicsFilt':

Usage

## 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")