Plot rmdFilt Object — plot.rmdFilt • pmartR

For plotting an S3 object of type 'rmdFilt'

# 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")