DescTools: PlotWeb – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

PlotWeb

Plot a Web of Connected Points

Description

This plot can be used to graphically display a correlation matrix by using the linewidth between the nodes in proportion to the correlation of two variables. It will place the elements homogenously around a circle and draw connecting lines between the points.

Usage

PlotWeb(m, col = c(hred, hblue), lty = NULL, lwd = NULL, args.legend=NULL,
        pch = 21, pt.cex = 2, pt.col = "black", pt.bg = "darkgrey",
        cex.lab = 1, las = 1, adj = NULL, dist = 0.5, ...)

Arguments

`m`	a symmetric matrix of numeric values
`col`	the color for the connecting lines
`lty`	the line type for the connecting lines, the default will be `par("lty")`.
`lwd`	the line widths for the connecting lines. If left to `NULL` it will be linearly scaled between the minimum and maximum value of `m`.
`args.legend`	list of additional arguments to be passed to the `legend` function. Use `args.legend = NA` if no legend should be added.
`pch`	the plotting symbols appearing in the plot, as a non-negative numeric vector (see `points`, but unlike there negative values are omitted) or a vector of 1-character strings, or one multi-character string.
`pt.cex`	expansion factor(s) for the points.
`pt.col`	the foreground color for the points, corresponding to its argument `col`.
`pt.bg`	the background color for the points, corresponding to its argument `bg`.
`las`	alignment of the labels, 1 means horizontal, 2 radial and 3 vertical.
`adj`	adjustments for the labels. (Left: 0, Right: 1, Mid: 0.5)
`dist`	gives the distance of the labels from the outer circle. Default is 2.
`cex.lab`	the character extension for the labels.
`...`	dots are passed to plot.

Details

The function uses the lower triangular matrix of m, so this is the order colors, linewidth etc. must be given, when the defaults are to be overrun.

Value

A list of x and y coordinates, giving the coordinates of all the points drawn, useful for adding other elements to the plot.

Author(s)

Andri Signorell <andri@signorell.net>

Examples

m <- cor(d.pizza[, which(sapply(d.pizza, IsNumeric, na.rm=TRUE))[-c(1:2)]],
         use="pairwise.complete.obs")
PlotWeb(m=m, col=c(hred, hblue), main="Pizza Correlation")


# let's describe only the significant corrs and start with a dataset
d.m <- d.pizza[, which(sapply(d.pizza, IsNumeric, na.rm=TRUE))[-c(1:2)]]

# get the correlation matrix
m <- cor(d.m, use="pairwise.complete.obs")

# let's get rid of all non significant correlations
ctest <- PairApply(d.m,  function(x, y) cor.test(x, y)$p.value, symmetric=TRUE)

# ok, got all the p-values, now replace > 0.05 with NAs
m[ctest > 0.05] <- NA
# How does that look like now?
Format(m, na.form = ". ", ldigits=0, digits=3, align = "right")

PlotWeb(m, las=2, cex=1.2)

# define line widths
PlotWeb(m, lwd=abs(m[lower.tri(m)] * 10))

DescTools

Tools for Descriptive Statistics

v0.99.41

GPL (>= 2)

Authors

Andri Signorell [aut, cre], Ken Aho [ctb], Andreas Alfons [ctb], Nanina Anderegg [ctb], Tomas Aragon [ctb], Chandima Arachchige [ctb], Antti Arppe [ctb], Adrian Baddeley [ctb], Kamil Barton [ctb], Ben Bolker [ctb], Hans W. Borchers [ctb], Frederico Caeiro [ctb], Stephane Champely [ctb], Daniel Chessel [ctb], Leanne Chhay [ctb], Nicholas Cooper [ctb], Clint Cummins [ctb], Michael Dewey [ctb], Harold C. Doran [ctb], Stephane Dray [ctb], Charles Dupont [ctb], Dirk Eddelbuettel [ctb], Claus Ekstrom [ctb], Martin Elff [ctb], Jeff Enos [ctb], Richard W. Farebrother [ctb], John Fox [ctb], Romain Francois [ctb], Michael Friendly [ctb], Tal Galili [ctb], Matthias Gamer [ctb], Joseph L. Gastwirth [ctb], Vilmantas Gegzna [ctb], Yulia R. Gel [ctb], Sereina Graber [ctb], Juergen Gross [ctb], Gabor Grothendieck [ctb], Frank E. Harrell Jr [ctb], Richard Heiberger [ctb], Michael Hoehle [ctb], Christian W. Hoffmann [ctb], Soeren Hojsgaard [ctb], Torsten Hothorn [ctb], Markus Huerzeler [ctb], Wallace W. Hui [ctb], Pete Hurd [ctb], Rob J. Hyndman [ctb], Christopher Jackson [ctb], Matthias Kohl [ctb], Mikko Korpela [ctb], Max Kuhn [ctb], Detlew Labes [ctb], Friederich Leisch [ctb], Jim Lemon [ctb], Dong Li [ctb], Martin Maechler [ctb], Arni Magnusson [ctb], Ben Mainwaring [ctb], Daniel Malter [ctb], George Marsaglia [ctb], John Marsaglia [ctb], Alina Matei [ctb], David Meyer [ctb], Weiwen Miao [ctb], Giovanni Millo [ctb], Yongyi Min [ctb], David Mitchell [ctb], Franziska Mueller [ctb], Markus Naepflin [ctb], Daniel Navarro [ctb], Henric Nilsson [ctb], Klaus Nordhausen [ctb], Derek Ogle [ctb], Hong Ooi [ctb], Nick Parsons [ctb], Sandrine Pavoine [ctb], Tony Plate [ctb], Luke Prendergast [ctb], Roland Rapold [ctb], William Revelle [ctb], Tyler Rinker [ctb], Brian D. Ripley [ctb], Caroline Rodriguez [ctb], Nathan Russell [ctb], Nick Sabbe [ctb], Ralph Scherer [ctb], Venkatraman E. Seshan [ctb], Michael Smithson [ctb], Greg Snow [ctb], Karline Soetaert [ctb], Werner A. Stahel [ctb], Alec Stephenson [ctb], Mark Stevenson [ctb], Ralf Stubner [ctb], Matthias Templ [ctb], Duncan Temple Lang [ctb], Terry Therneau [ctb], Yves Tille [ctb], Luis Torgo [ctb], Adrian Trapletti [ctb], Joshua Ulrich [ctb], Kevin Ushey [ctb], Jeremy VanDerWal [ctb], Bill Venables [ctb], John Verzani [ctb], Pablo J. Villacorta Iglesias [ctb], Gregory R. Warnes [ctb], Stefan Wellek [ctb], Hadley Wickham [ctb], Rand R. Wilcox [ctb], Peter Wolf [ctb], Daniel Wollschlaeger [ctb], Joseph Wood [ctb], Ying Wu [ctb], Thomas Yee [ctb], Achim Zeileis [ctb]

Initial release

2021-04-09