plot.isobaricnormRes {pmartR}

Plot isobaricnormRes object

Description

Creates box plots for an S3 object of type 'isobaricnormRes'

Usage

## S3 method for class 'isobaricnormRes'
plot(
  x,
  order = FALSE,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = NULL,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "none",
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Arguments

x

an object of type isobaricnormRes, created by normalize_isobaric with apply_norm = FALSE

order

logical value. If TRUE the samples will be ordered by the column of f_data containing the experiment/plate information.

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".

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)
myiso <- edata_transform(omicsData = isobaric_object, data_scale = "log2")
result <- normalize_isobaric(myiso,
  exp_cname = "Plex",
  apply_norm = FALSE,
  refpool_cname = "Virus",
  refpool_notation = "Pool"
)
plot(result)