mdaplot: Plotting function for a single set of objects
In mdatools: Multivariate Data Analysis for Chemometrics

mdaplot

R Documentation

Plotting function for a single set of objects

Description

mdaplot is used to make different kinds of plot for one set of data objects.

Usage

mdaplot(
  data = NULL,
  ps = NULL,
  type = "p",
  pch = 16,
  col = NULL,
  bg = par("bg"),
  bwd = 0.8,
  border = NA,
  lty = 1,
  lwd = 1,
  cex = 1,
  cgroup = NULL,
  xlim = NULL,
  ylim = NULL,
  colmap = "default",
  labels = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  show.labels = FALSE,
  show.colorbar = !is.null(cgroup),
  show.lines = FALSE,
  show.grid = TRUE,
  grid.lwd = 0.5,
  grid.col = "lightgray",
  show.axes = TRUE,
  xticks = NULL,
  yticks = NULL,
  xticklabels = NULL,
  yticklabels = NULL,
  xlas = 0,
  ylas = 0,
  lab.col = "darkgray",
  lab.cex = 0.65,
  show.excluded = FALSE,
  col.excluded = "#C0C0C0",
  nbins = 60,
  force.x.values = NA,
  opacity = 1,
  pch.colinv = FALSE,
  ...
)

Arguments

`data`	a vector, matrix or a data.frame with data values.
`ps`	'plotseries' object, if NULL will be created based on the provided data values
`type`	type of the plot ("p", "d", "l", "b", "h", "e").
`pch`	a character for markers (same as `plot` parameter).
`col`	a color for markers or lines (same as `plot` parameter).
`bg`	background color for scatter plots wich 'pch=21:25'.
`bwd`	a width of a bar as a percent of a maximum space available for each bar.
`border`	color for border of bars (if barplot is used)
`lty`	line type
`lwd`	line width
`cex`	scale factor for the marker
`cgroup`	a vector with values to use for make color groups.
`xlim`	limits for the x axis (if NULL, will be calculated automatically).
`ylim`	limits for the y axis (if NULL, will be calculated automatically).
`colmap`	a colormap to use for coloring the plot items.
`labels`	a vector with text labels for data points or one of the following: "names", "indices", "values".
`main`	an overall title for the plot (same as `plot` parameter).
`xlab`	a title for the x axis (same as `plot` parameter).
`ylab`	a title for the y axis (same as `plot` parameter).
`show.labels`	logical, show or not labels for the data objects.
`show.colorbar`	logical, show or not colorbar legend if color grouping is on.
`show.lines`	vector with two coordinates (x, y) to show horizontal and vertical line cross the point.
`show.grid`	logical, show or not a grid for the plot.
`grid.lwd`	line thinckness (width) for the grid.
`grid.col`	line color for the grid.
`show.axes`	logical, make a normal plot or show only elements (markers, lines, bars) without axes.
`xticks`	values for x ticks.
`yticks`	values for y ticks.
`xticklabels`	labels for x ticks.
`yticklabels`	labels for y ticks.
`xlas`	orientation of xticklabels.
`ylas`	orientation of yticklabels.
`lab.col`	color for data point labels.
`lab.cex`	size for data point labels.
`show.excluded`	logical, show or hide rows marked as excluded (attribute 'exclrows').
`col.excluded`	color for the excluded objects (rows).
`nbins`	if scatter density plot is shown, number of segments to split the plot area into. (see also ?smoothScatter)
`force.x.values`	vector with corrected x-values for a bar plot (do not specify this manually).
`opacity`	opacity for plot colors (value between 0 and 1).
`pch.colinv`	allows to swap values for 'col' and 'bg' for scatter plots with 'pch' valyes from 21 to 25.
`...`	other plotting arguments.

Details

Most of the parameters are similar to what are used with standard plot function. The differences are described below.

The function makes a plot of one set of objects. It can be a set of points (scatter plot), bars, lines, scatter-lines, errorbars og an image. The data is organized as a data frame, matrix or vector. For scatter and only first two columns will be used, for bar plot only values from the first row. It is recommended to use mda.subset method if plot should be made only for a subset of the data, especially if you have any excluded rows or columns or other special attributed, described in the Bookdown tutorial.

If data is a data frame and contains one or more factors, they will be converted to a dummy variables (using function mda.df2mat) and appears at the end (last columns) if line or bar plot is selected.

The function allows to colorize lines and points according to values of a parameter cgroup. The parameter must be a vector with the same elements as number of objects (rows) in the data. The values are divided into up to eight intervals and for each interval a particular color from a selected color scheme is assigned. Parameter show.colorbar allows to turn off and on a color bar legend for this option.

The used color scheme is defined by the colmap parameter. The default scheme is based on color brewer (colorbrewer2.org) diverging scheme with eight colors. There is also a gray scheme (colmap = "gray") and user can define its own just by specifing the needed sequence of colors (e.g. colmap = c("red", "yellow", "green"), two colors is minimum). The scheme will then be generated automatically as a gradient among the colors.

Besides that the function allows to change tick values and corresponding tick labels for x and y axis, see Bookdown tutorial for more details.