plot-dimRes: Plot dimRes Object

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

Plot dimRes Object

Description

For plotting an S3 object of type 'dimRes'

Usage

## S3 method for class 'dimRes'
plot(
  x,
  omicsData = NULL,
  color_by = NULL,
  shape_by = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 0,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  point_size = 4,
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Arguments

x	object of class dimRes created by the dim_reduction function
omicsData	optional omicsData for use in specifying a column name in fdata when using color_by or shape_by.
color_by	character string specifying which column to use to control the color for plotting. NULL indicates the default value of the main effect levels (if present). "Group" uses the "Group" column of group_DF. NA indicates no column will be used, and will use the default theme color. If an omicsData object is passed, any other value will use the specified column of f_data.
shape_by	character string specifying which column to use to control the shape for plotting. NULL indicates the default value of the second main effect levels (if present). "Group" uses the "Group" column of group_DF. NA indicates no column will be used, and will use the default theme shape. If an omicsData object is passed, any other value will use the specified column of f_data.
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 0.
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 4.
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.
...	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)

mylipid <- edata_transform(omicsData = lipid_neg_object, data_scale = "log2")
mylipid <- group_designation(omicsData = mylipid, main_effects = "Virus")
pca_lipids <- dim_reduction(omicsData = mylipid)
plot(pca_lipids)


myseq <- group_designation(omicsData = rnaseq_object, main_effects = "Virus")
pca_seq <- dim_reduction(omicsData = myseq)
plot(pca_seq)

pmartR/pmartR documentation built on March 4, 2024, 8:32 a.m.