plotlowertri: Generate a graphs showing correlation matrix (lower semi...
In helixcn/spaa: SPecies Association Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Generate graphs (lower semi matrix) showing lower semi matrix. These graphs are often used to show the structure of a correlation, similarity or dissimilarity matrix.

plotlowertri(input, valuename = "r",
pchlist = c(19, 17, 15, 1, 5, 2, 7), interval = 6,
cex = 1, ncex = 1, int =1.2, add.number = TRUE,
size = FALSE, add.text = FALSE, show.legend = TRUE,
digits = 2)

`input`	The `input`, often a correlation or a distance matrix.
`valuename`	Name of the value that to show in the legend.
`pchlist`	A numberic vector specifying the shapes of points, see `pch par()`.
`interval`	Types of point shapes to show
`cex`	A number specifying the text size in the legend
`ncex`	Size of the text shown above each column.
`int`	Space between lines within the legend
`add.number`	If the column number should be shown
`size`	Whether the size of points should change with the value
`add.text`	Logical, If the number should be shown in the grid.
`show.legend`	Logical, If the legend should be appear.
`digits`	Number of digits for the label of each interval.

In the legend, space between lines could be adjusted by specifying int.

lower matrix plot

Jinlong Zhang jinlongzhang01@gmail.com

Zhang Qiaoying, Peng Shaolin, Zhang Sumei, Zhang Yunchun, Hou Yuping.(2008). Association of dormintant species in Guia hill Municipal Park of Macao. Ecology and Environment. 17:1541-1547

See Also plotnetwork

data(testdata)
spmatrix <- data2mat(testdata)
result <- sp.pair(spmatrix)

## Check the legend for 0.00 to 0.33 (Unwanted label)
plotlowertri(result$Pearson, int = 0.5, cex=1.5)
title("Pearson Correlation Lower Matrix Plot")

## Change the size of points and reset the intervals.
## Warning: The lower matrix plot illustrating Pearson
## Correlation between each pair of species. Note the
## triangle didn't appeared in the plots, but have been
## added to the legend. This is due to the distribution
## of data. Be careful in selection of intervals.


plotlowertri(result$Pearson, int = 0.5, cex=1.5,
interval = 4, pchlist = c(19, 17, 15, 1, 5), size = TRUE)

title("Pearson Correlation Lower Matrix Plot")

## "Pure" dots, may have to add legend manually...
plotlowertri(result$Pearson, int = 0.5, cex=2.5,
interval = 4, pchlist = rep(19, 5), size = TRUE,
show.legend = FALSE)

title("Pearson Correlation Lower Matrix Plot")


## Using BCI data
library(vegan)
data(BCI)
## select the top 30 species according to relative frequency.
sub <- sub.sp.matrix(BCI, common = 30)
## Original
plotlowertri(cor(sub))

## Change size
plotlowertri(cor(sub), size = TRUE, cex = 3)

## Set the digits to 1
plotlowertri(cor(sub), size = TRUE, cex = 3, digits = 1,
ncex = 0.7)