pmartR (version 2.4.6)

plot.nmrnormRes: Plot nmrnormRes Object

Description

Creates a scatter plot for an S3 object of type 'nmrnormRes'

Usage

# S3 method for nmrnormRes
plot(
  x,
  nmrData = NULL,
  order_by = NULL,
  color_by = 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 = "none",
  point_size = 2,
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Value

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

Arguments

x

an object of type nmrnormRes, created by normalize_nmr

nmrData

An nmrData object.

order_by

A character string specifying a column in f_data by which to order the samples.

color_by

A character string specifying a column in f_data by which to color the points.

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

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.

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

integer specifying the size of the points. The default is 2.

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)
mynmr <- edata_transform(omicsData = nmr_identified_object, data_scale = "log2")
mynmrnorm <- normalize_nmr(
  omicsData = mynmr,
  apply_norm = FALSE,
  metabolite_name = "unkm1.53"
)
plot(mynmrnorm)

mynmrnorm2 <- normalize_nmr(
  omicsData = mynmr,
  apply_norm = FALSE,
  sample_property_cname = "Concentration"
)
plot(mynmrnorm2)
}