Plot dimRes Object — plot.dimRes • pmartR

For plotting an S3 object of type 'dimRes'

# 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)

# \donttest{
myseq <- group_designation(omicsData = rnaseq_object, main_effects = "Virus")
pca_seq <- dim_reduction(omicsData = myseq)
plot(pca_seq)
# }