plotnetwork: Plot correlation network (Deprecated)

In helixcn/spaa: SPecies Association Analysis

Description

Plotting correlation network showing the relationship between each pair of sites connected by segments. The points are arranged in a circle.

Usage

plotnetwork(datainput, n_levels = 6, xlim = c(-2.5, 5),
    ylim = c(-2.5, 2.5), node_size = 3, lwd.var = TRUE,
    lwd = 4, label_dist = 1.2,
    show.node = TRUE, show.text.label = TRUE,
    linecol = c("orange", "blue"),show.legend = TRUE,
    valuename = "r", legendx = 3,
    legendy = -2, legend_line_space = 1,
    legend_linelength = 0.3, adjust_legend_x = 0,
    adjust_legend_y = 0,digits = 2, ... )

Arguments

datainput	The correlation matrix, usually a lower matrix
n_levels	Number of types of segments to show the correlation, note interval should <12
xlim	horizontal range of the canvas
ylim	vertical range of the canvas
node_size	size of the nodes
lwd.var	logical, if the segments width should vary with the absolute value
lwd	width of the segments for connecting the sites, default 1
label_dist	Distance of text labels from each node.
show.node	Whether the nodes in the figure should be labeled
show.text.label	Whether the text label should be drawn.
linecol	Colours showing positve or negative correlation. The lines representing positive correlations use the first element
show.legend	If the legend should be shown
valuename	Name of the variable shown in the legend
legendx	the starting position of the legend x
legendy	the starting position of the legend y
legend_line_space	the space between the lines in the legend
legend_linelength	length of the segment in the legend
adjust_legend_x	adjusting the position of legend (x)
adjust_legend_y	adjusting the position of legend (y)
digits	Number of disgits shown in the legend, it will be used in generating the breaks as well
...	other parameters related with plot.default

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 orange or blue, according the sign of the value.

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("red", "black"))

plotnetwork(result$Pearson, n_levels = 4,  node_size = 4,  
    lwd.var = FALSE, label_dist = 0.8, show.node = FALSE, 
    show.text.label = FALSE, linecol = c("red", "black"), 
    show.legend = TRUE, valuename = "r", legendx = 3, 
    legend_line_space = 0.5, legend_linelength = 0.5, 
    adjust_legend_x = -1)

title("Pearson Correlation Network")

helixcn/spaa documentation built on Aug. 13, 2021, 3:21 a.m.