pmartR (version 2.4.6)

plot.normRes: Plot normRes Object

Description

For plotting an S3 object of type 'normRes'

Usage

# S3 method for normRes
plot(
  x,
  order_by = NULL,
  color_by = NULL,
  facet_by = NULL,
  facet_cols = 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",
  ylimit = NULL,
  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

normRes object created by the normalize_global function

order_by

character string specifying the column name of f_data by which to order the boxplots. If order_by is "Group", the boxplots will be ordered by the group variable from the group_designation function. If NULL (default), the boxplots will be displayed in the order they appear in the data.

color_by

character string specifying the column name of f_data by which to color the boxplots. If color_by is "Group", the boxplots will be colored by the group variable from the group_designation function. If NULL (default), the boxplots will have one default color.

facet_by

character string specifying the column name of f_data with which to create a facet plot. Default value is NULL.

facet_cols

optional integer specifying the number of columns to show in the facet plot.

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".

ylimit

numeric vector of length 2 specifying y-axis lower and upper limits.

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"
)
norm_object <- normalize_global(
  omicsData = mymetab,
  subset_fn = "all",
  norm_fn = "median"
)
plot(norm_object, order_by = "Phenotype", color_by = "Phenotype")
}