pmartR (version 2.5.1)

plot.rmdFilt: Plot rmdFilt Object

Description

For plotting an S3 object of type 'rmdFilt'

Usage

# S3 method for rmdFilt
plot(
  x,
  pvalue_threshold = NULL,
  sampleID = NULL,
  order_by = NULL,
  color_by = NULL,
  interactive = FALSE,
  hist = 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,
  ...
)

Value

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

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 or hist is TRUE, . 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. Only applicable where sampleID = NULL and hist = FALSE.

color_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 color_by is "Group" or NULL, the plot will be colored by the group variable from the group_designation function. Only applicable where sampleID = NULL.

interactive

logical value. If TRUE produces an interactive plot.

hist

boolean value that changes default scatter plot to a histogram displaying the distribution of all used RMD metrics.

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.

Examples

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