Pleiad: Correlation circles (correlation pleiads)

In shipunov: Miscellaneous Functions from Alexey Shipunov

Correlation circles (correlation pleiads)

Description

Plot correlation circles (correlation pleiads, correlograms)

Usage

Pleiad(tbl, abs=FALSE, corr=FALSE, dist=FALSE, treshold=FALSE,
 circ=list(1, 1, 1), breaks=5, auto=TRUE, gr=6, lwd=NULL, lty=NULL,
 lcol=NULL,  abbr=-1, lbltext="internal", lblcex=1, off=1.09, hofft=0.07,
 hoff=1.02, legend=TRUE,  legtext=1, legpos="topright", leghoriz=FALSE,
 show.int=FALSE, dig.lab=1, neg.col=NULL, ...)

Arguments

tbl	Data: square, numeric, symmetric matrix with same row and column names
abs	If TRUE, uses absolute values instead of real
corr	If TRUE, uses absolute values instead of real and cuts from 0 to 1, this is good for correlation matrices
dist	If TRUE, converts distance matrix to the data frame – good for "dist" objects
treshold	If this is (saying) =.5, selects for plotting (with lty=1) only those values which are >.5
circ	Line type, width and color for the cirle; if first or third =0, no cicrle
breaks	How to cut() values, if "cramer", then =c(0, .1, .3, .5, 1)
auto	If FALSE, specify 'lwd', 'lty' and 'lcol'
gr	Grayscale scheme starts from 6 breaks
lwd	If auto=FALSE, specify here the vector concerted with breaks
lty	If auto=FALSE, specify here the vector concerted with breaks
lcol	If auto=FALSE, specify here the vector concerted with breaks; if length(lcol) == 1, all lines are of particular color
abbr	If =-1, no abbreviation; if =0, no labels; other values run abbreviate(..., abbr)
lbltext	If this is a vector starting from something else, will replace dimnames
lblcex	Magnification of labels
off	Radial offset of labels, be careful!
hofft	Treshold determining which labels are rigtmost/leftmost, 'hofft=0' put all labels into this group
hoff	Horizontal offset for rightmost/leftmost labels; 'hoff=1' removes offset
legend	If FALSE, no legend
legtext	If =1 then "weaker ... stronger"; if =2, shows cutting intervals; if =3, then 1:5; if >3, issues error
legpos	Position of the legend, see help(legend)
leghoriz	Make the legend horizontal?
show.int	Show intervals in (...] form
dig.lab	dig.lab for cut(), use to change notation
neg.col	If not NULL and 'abs' or 'corr' are TRUE, colorize negative correlations using specified color
...	Further arguments to points()

Details

Correlation circles (correlation pleiads, correlograms) based on the works of Petr Terentjev's (Saint-Petersburg) school.

Please be sure to use 'corr=TRUE' or 'dist=TRUE' when working with correlation matrices or 'dist' objects, respectively.

It is probably a good idea to order data entries with hierarchical clustering to optimize the resulted graph (see examples).

Note that: (1) 'lty', 'lwd' and 'lcol' are not recycling; (2) plot has no margins so consider second 'legend()' to add any text to the plot (see examples); (3) it works best when number of items is relatively low (< 30); (4) it can visualize (colorize) negative correlations (see examples) but this works bes with default (black) color; (5) 'dist=TRUE' will convert dissimilarities into similarities by substracting from maximum.

Alternatives: those graph plotting packages which are able to plot "correlogram".

Value

Data frame (invisibly) with position of points, might help in plot enchancing.

Author(s)

Alexey Shipunov

Examples

l.c <- cor(datasets::longley, method="spearman", use="pairwise")
Pleiad(l.c, corr=TRUE, legtext=2, pch=21, cex=2, bg="white", breaks=3,
 gr=3, hoff=1, show.int=TRUE)
legend("topleft", legend="Macroeconomic correlations", text.font=2,
bty="n")

## colorize negative correlations and use hclust() to re-order
reorder <- hclust(dist(t(longley)))$order
Pleiad(l.c[reorder, reorder], corr=TRUE, neg.col="red")

dr.c <- cor(drosera[, -1], method="spearman", use="pairwise")
## simple example with most defaults
Pleiad(dr.c, corr=TRUE)
## complex example with user-specified colors etc.
Pleiad(dr.c, corr=TRUE, legtext=2, pch=19, cex=1.2, hoff=1.06,
 auto=FALSE, lwd=c(1, 1, 1, 2.5, 4), lty=rep(1, 5),
 lcol=colorRampPalette(c("grey", "#D8284F"))(5),
 circ=c(2, 1, 1))

## visualize distances
Pleiad(dist(t(atmospheres)), dist=TRUE, breaks=3, legtext=2, dig.lab=3)

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.