# Plot correlation network (Deprecated)

`plotnetwork.Rd`

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

    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.

## References

None

## Author

Jinlong Zhang jinlongzhang01@gmail.com

## 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")