plotZ: Comparison of Z scores between two PANDA runs

In jnpaulson/pandaR: PANDA Algorithm

Comparison of Z scores between two PANDA runs

Description

Given two PANDA objects with the same network structure, plot the Z-score comparison. The two PANDA objects should only differ in the gene expression used for the network constructions or other parameters.

Usage

plotZ(x, y, hex = TRUE, bins = 200, addLine = TRUE, rank = FALSE)

Arguments

x	PANDA object - output of the panda function.
y	PANDA object - second PANDA object.
hex	TRUE/FALSE - If TRUE, bin data points to avoid over plotting.
bins	Number of bins to use for plotting.
addLine	TRUE/FALSE - to add y=x line.
rank	TRUE/FALSE - If TRUE, plot rank of edge weights rather than weight values.

Value

ggplot comparing the Z-scores between the two networks.

Examples

data(pandaResult)
data(pandaToyData)
pandaRes <- pandaRes2 <- pandaResult
plotZ(pandaRes, pandaRes2)


panda.res1 <- with(pandaToyData, panda(motif, expression, ppi, hamming=1))
panda.res2 <- with(pandaToyData, panda(motif, expression + 
                   rnorm(prod(dim(expression)),sd=5), ppi, hamming=1))
plotZ(panda.res1, panda.res2,addLine=FALSE)

jnpaulson/pandaR documentation built on May 13, 2024, 11:30 a.m.