plotnetwork: Correlation network plot

In spaa: SPecies Association Analysis

Description

This function could be used to plot correlation network, with less than 15 sites (recommended). The points lie in a circle with lines connected. Blue lines indicate negative values and the red ones the positive ones.

Usage

plotnetwork(datainput, interval = 8, xlim = c(-2.5,5), 
ylim=c(-3.2,3.2), lty = c(1,2,3,4,4,3,2,1,5), value = "r", 
legendx = 3, legendy = 0, right = 1.2, intcept = 0.22, 
left = 0.35, linelength = 0.3, cex = 3, lwd = 1.5, 
show.legend = TRUE, digits = 2, dit = 1.2, 
number.label = TRUE, text.label = TRUE, 
linecol = c("red", "black"), ...)

Arguments

datainput	The correlation matrix, ex. Pearson's correlation matrix
interval	Number of intervals of the values, indicating how to partition the range of input data
xlim	The x range of the plot. The users need not to change it.
ylim	The y range of the plot. The users need not to change it.
lty	Line styles used in connection lines for each interval. Must have number of elements + 1.
value	Value of the matrix, should be a character, will used in legend.
legendx	Legend position x.
legendy	Legend position y.
right	Legend position adjustment parameter.
intcept	Legend position adjustment. can be used to specify the row space between each line for the legend.
left	Legend position adjustment parameter.
linelength	Line length in the legend.
cex	Point size for each circle.
lwd	Line width for each circle.
...	Other arguments to be passed from.
show.legend	Whether the legend should be drawn.
digits	Number of digits displayed in legend.
dit	Distance of text labels from each corner.
number.label	Whether the number label should be drawn.
text.label	Whether the text label should be drawn.
linecol	Colours of the lines specified. The positive correlation will be drawn in the first colour specified.

Details

This function could be used to plot the pairwise connections between less than 20 sites ( above 20 is not recommended since there would be too many connections).

The lines will be in red or blue, according the sign of the value of association. Users can adjust the line style and legends based on their requirements.

Value

Correlation network plots.

Author(s)

Jinlong Zhang [e-mail]

References

None

Examples

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

plotnetwork(result$Pearson, linecol = c("orange", "blue"),
number.label = FALSE)

title("Pearson Correlation Network")

Example output

spaa documentation built on May 2, 2019, 9:44 a.m.