plot-rmdFilt: Plot rmdFilt Object

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

Plot rmdFilt Object

Description

For plotting an S3 object of type 'rmdFilt'

Usage

## S3 method for class 'rmdFilt'
plot(
  x,
  pvalue_threshold = NULL,
  sampleID = NULL,
  order_by = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 90,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  point_size = 3,
  bw_theme = TRUE,
  palette = NULL,
  use_VizSampNames = FALSE,
  ...
)

Arguments

x	object of class rmdFilt created via rmd_filter
pvalue_threshold	numeric threshold for the Robust Mahalanobis Distance (RMD) p-value. If sampleID is NULL (see sampleID below), a horizontal line is plotted at the RMD value that corresponds with the threshold, and all samples above the line have a p-value below the threshold. If sampleID is not NULL, pvalue_threshold will do nothing. Default value is NULL.
sampleID	character vector specifying the sample names to be plotted. If specified, the plot function produces a boxplot instead of a scatterplot. A point, colored by sample, will be placed on each boxplot for that sample's value for the given metric. The default value is NULL.
order_by	character string specifying a variable by which to order the samples in the plot. This variable must be found in the column names of fdata from the rmdFilt object. If order_by is "Group", the plot will be ordered by the group variable from the group_designation function. If NULL (default), the samples will be displayed in the order in which they first appear.
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 90.
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".
point_size	An integer specifying the size of the points. The default is 3.
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.
use_VizSampNames	logical value. Indicates whether to use custom sample names. The default is FALSE.
...	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)
mymetab <- edata_transform(omicsData = metab_object, data_scale = "log2")
mymetab <- group_designation(omicsData = mymetab, main_effects = "Phenotype")
rmd_results <- rmd_filter(omicsData = mymetab, metrics = c("MAD", "Skewness", "Correlation"))
plot(rmd_results, pvalue_threshold = 0.0001, order_by = "Phenotype")

pmartR documentation built on June 10, 2025, 9:10 a.m.