Make a SuperPlot

The function superplot() creates a SuperPlot using ggplot2. At a minimum the user needs to supply a data frame with at least three columns that have the measurement (meas), condition (cond) and replicate (repl) information. There are direct arguments to change the colours, axes labels, sizes, and more (see details below). There is also a flexible options argument to supply a list to specify even more customisation.

If you are building a very complicated SuperPlot, it is preferable to specify a superplot_spec using superplot_spec() and sp_modify() before plotting with autoplot()

Usage

superplot(
  df,
  meas,
  cond,
  repl,
  facet = NULL,
  pal = "tol_bright",
  pal_order = NULL,
  xlab = "",
  ylab = "Measurement",
  datadist = "sina",
  size = c(2, 3),
  alpha = c(0.5, 0.7),
  bars = "mean_sd",
  linking = FALSE,
  rep_summary = "rep_mean",
  shapes = FALSE,
  fsize = 12,
  gg = NULL,
  stats = FALSE,
  stats_test = "para_unpaired",
  info = FALSE,
  options = NULL
)

Arguments

df

data frame with at least three columns: meas, cond, repl

meas

character name of column with measurement (e.g. intensity)

cond

character name of column with condition (e.g. Control, WT)

repl

character name of column with replicate (e.g. unique experiment identifiers)

facet

character name of column to facet by (default is NULL)

pal

name of colour palette to use (default is "tol_bright")

pal_order

optional order of the palette colours: NULL (default), "reverse", "random" (the order used is printed so it can be reused), or an integer vector containing a permutation of the sequence of numbers from 1 to the total

xlab

string for x label (default is empty)

ylab

string for y label (default is "Measurement")

datadist

string for data distribution to use, select ("sina" default, "jitter", or "violin")

size

numeric vector of size range data and summary points (default is c(2, 3))

alpha

numeric vector of alpha range data and summary points (default is c(0.5, 0.7))

bars

string for type of error bars to add, select "mean_sd" (default), "mean_sem", or "mean_ci"; for no bars use an empty string (""); for no error bars but still show the mean with a crossbar, use "none".

linking

logical for whether to link summary points between conditions (default is FALSE)

rep_summary

string for summary statistic to use for replicates, select ("rep_mean" default, or "rep_median")

shapes

logical for whether to use different shapes for replicates

fsize

numeric font size for text (default is 12)

gg

ggplot object to add to (default is NULL)

stats

logical for whether to add statistical tests (default is FALSE)

stats_test

string for statistical test to use, select ("para_unpaired", "para_paired", "nonpara_unpaired", or "nonpara_paired")

info

logical for whether to print information about the plot (default is FALSE)

options

optional named list for advanced layer customization. See superplot_spec() and sp_modify() for available options.

Value

ggplot object

Examples

superplot(lord_jcb,
  "Speed", "Treatment", "Replicate",
  ylab = "Speed (um/min)")