scatterPlot: Making a scatter plot of x against y, colour coded by z.
In wanyuac/handyR: Handy functions for R programming.

scatterPlot

R Documentation

Making a scatter plot of x against y, colour coded by z.

Description

Model: y ~ x.

Usage

scatterPlot(
  x,
  y,
  z,
  x.bg = NA,
  y.bg = NA,
  z.bg = NA,
  log = "both",
  log.base = 10,
  replace.zero = 1e-05,
  breaks.min = 0,
  breaks.max = 1,
  breaks.n = 51,
  col.grad = c("blue", "green", "red"),
  log.z = FALSE,
  log.z.base = 10,
  output = "plot.png",
  w = 800,
  h = 640,
  title = "Y~X",
  x.lab = "X",
  y.lab = "Y",
  cex.main = 1.5,
  cex.lab = 1.5,
  cex.axis = 1.5,
  x.extension = c(0, 0),
  y.extension = c(0, 0),
  margin = c(4.5, 4.5, 3, 2),
  joint.col = FALSE,
  col.bg = "grey",
  pch.bg = 1,
  cex.bg = 1,
  pch = 19,
  cex = 1,
  show.range = FALSE,
  x.range = NA,
  x.bg.range = NA,
  range.pch = ".",
  cex.range = 1,
  add.line = FALSE,
  line.a = NULL,
  line.b = NULL,
  line.h = NULL,
  line.v = NULL,
  line.style = 3,
  line.col = "grey",
  turnoff.dev = TRUE
)

Arguments

`x`	explanatory variable of your interest to be plotted.
`y`	response variable of your interest to be plotted.
`z`	the variable for generating a colour gradient. It is in the same order of both x and y.
`x.bg`	and y.bg: background values of X and Y respectively to be contrasted with x and y. The function makes a scatter plot of x.bg and y.bg at first.
`z.bg`	the variable for coding colours of (X.bg, Y.bg) with the same colour gradient defined by c(z, z.bg). In practice, x, y and z are three columns of the same data frame. log = c("both", "x", "y", "none"), determines whether to apply logarithmic transformation to x or y.
`log.base`	the base for logarithmic transformation. The default transformtion takes log10.
`replace.zero`	a small value used for replacing zero values before taking logarithms. Only takes effect if log != "none".
`breaks.min`	and breaks.max determine the lower bound and upper bound for factorising the variable z.
`breaks.n`	the number of breaks for dividing z into levels. The number of colour gradients is n-1.
`col.grad`	a vector of characters defining boundaries of the colour gradient.
`log.z`	whether to take the same logarithmic transformation for both z and z.bg.
`log.z.base`	the base for the logarithmic transformation of z and z.bg.
`output`	the name of the output PNG file.
`w`	define the width of the output picture.
`h`	define the height of the output picture.
`title`	configure the title of the plot.
`x.lab`	configure the label of X axis of the plot.
`y.lab`	configure the label of Y axis of the plot.
`cex.main`	cex.lab and cex.axis set the sizes of the title, labels and axes of the plot.
`x.extension`	and y.extension configure the extensions to the left/lower and right/upper sides of the plot.
`margin`	a vector of integers to be passed to par(mar = margin). For example, x.extension = c(-1, 1).
`joint.col`	whether to colour all data points with the same colour gradient. Remember to check the break.min and breaks.max when you are using this option.
`col.bg`	will be overridden if joint.col == TRUE.
`pch`	and cex define the point style and size of data points of interests (Y ~ X).
`show.range`	whethter to plot values from which an x is calculated. In this case, X is a summary statistic.
`x.range`	a vector of characters separated by commas, containing every value that generating an X. For example, x.range = c("1,2,3", "2,2,5")
`x.bg.range`	the same kind of vector as x.range for background X values.
`range.pch`	and cex.range determine the type and size of points for values in x.range.
`add.line`	determines whether to add a guideline to the plot.
`line.style`	the lty argument for abline(.)
`line.col`	the colour of the guideline.
`turnoff.dev`	not to call dev.off() if turnoff.dev = FALSE so that a user can add more features to the plot.
`line.a/b/h/v`	four arguments (a, b, h, v) to be passed to R's build-in function abline.