mdatools (version 0.7.0)

mdaplot: Plotting function for a single set of objects

Description

mdaplot is used to make a scatter, line or a bar plot for one set of data objects.

Usage

mdaplot(data, type = "p", pch = 16, col = NULL, lty = 1, lwd = 1, bwd = 0.8, cgroup = NULL, xlim = NULL, ylim = NULL, colmap = "default", labels = NULL, main = NULL, xlab = NULL, ylab = NULL, single.x = T, show.labels = F, show.colorbar = T, show.lines = F, show.grid = T, show.axes = T, xticks = NULL, xticklabels = NULL, yticks = NULL, yticklabels = NULL, lab.col = "darkgray", lab.cex = 0.65, ...)

Arguments

data

a matrix with data values.

type

type of the plot ('p', 'l', 'b', 'h').

pch

a character for markers (same as plot parameter).

col

a color for markers or lines (same as plot parameter).

lty

the line type (same as plot parameter).

lwd

the line width (thickness) (same as plot parameter).

bwd

a width of a bar as a percent of a maximum space available for each bar.

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 (if NULL, row names will be used).

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).

single.x

logical, is first column of data matrix used for x values (or every odd)?

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.

show.axes

logical, make a normal plot or show only elements (markers, lines, bars) without axes.

xticks

tick values for x axis.

xticklabels

labels for x ticks.

yticks

tick values for y axis.

yticklabels

labels for y ticks.

lab.col

color for data point labels.

lab.cex

size for data point labels.

...

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 or scatter-lines. The data is organized as a matrix. For scatter and bar plot only two columns are needed, but to plot set of lines there are two ways to organise the data matrix.

If parameter single.x = T it means first column of the matrix contains x values, as the other columns contain y values (one column - one line, e.g. [x y1 y2 y3]). If single.x = F it means every odd column of matrix contains x values and every even column - y values of a line (e.g. [x1 y1 x2 y2 x3 y3]). This option is needed if lines have different x values.

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 examples for more details.

See Also

mdaplotg - to make for several sets of data objects (groups of objects).

Examples

library(mdatools)
### Examples of using mdaplot function

## 1. Make a line plot for y = x^2 with different x values for each line

x1 = seq(-10, 10, length = 100)
y1 = x1^2
x2 = seq(-9, 9, length = 100) + 1
y2 = x2^2 * 1.2
x3 = seq(-8, 8, length = 100) + 2
y3 = x3^2 * 1.4

mdaplot(cbind(x1, y1, x2, y2, x3, y3), type = 'l', single.x = FALSE)

## 2. Change tick values and labels for x axis
mdaplot(cbind(x1, y1, x2, y2, x3, y3), type = 'l', single.x = FALSE,
        xticks = c(-8, 0, 8), xticklabels = c('Negative', 'Zero', 'Positive'))


## 3. Make a line plot of the spectra with coloring by concentration of first component
## using different color maps

data(simdata)

# first column of matrix val will contain the wavelength
# and the last columns - spectra from calibration set
val = cbind(simdata$wavelength, t(simdata$spectra.c))

# concentration will be used for color groups
c1 = simdata$conc.c[, 1]

par(mfrow = c(2, 2))
mdaplot(val, type = 'l', cgroup = c1)
mdaplot(val, type = 'l', cgroup = c1, colmap = 'gray', show.colorbar = FALSE)
mdaplot(val, type = 'l', cgroup = c1, colmap = c('red', 'green'))
mdaplot(val, type = 'l', cgroup = c1, colmap = c('#ffff00', '#00ffff'))
par(mfrow = c(1, 1))

## 3. Show scatter plots from spectral data with color groups and other parameters
## see how limits are adjusted if show.lines option is used

nobj = 30
# concentration is used for color groups
c1 = simdata$conc.c[1:nobj, 1]
# x values are absorbance of waveband 100, y values - absorbance for waveband 110
pdata = cbind(
   simdata$spectra.c[1:nobj, 100, drop = FALSE],
   simdata$spectra.c[1:nobj, 110, drop = FALSE])

par(mfrow = c(2, 2))
mdaplot(pdata, cgroup = c1, main = 'Spectra', show.lines = c(0.1, 0.06))
mdaplot(pdata, cgroup = c1, main = 'Spectra', show.lines = c(0.06, 0.01))
mdaplot(pdata, cgroup = c1, xlab = '309 nm', ylab = '319 nm', main = 'Spectra', show.labels = TRUE)
mdaplot(pdata, col = 'red', pch = 17, show.labels = TRUE, labels = paste('Obj', 1:nobj))
par(mfrow = c(1, 1))