pmartR (version 2.4.6)

plot.dimRes: Plot dimRes Object

Description

For plotting an S3 object of type 'dimRes'

Usage

# S3 method for 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,
  ...
)

Value

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

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.

Examples

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