SMITE (version 1.0.2)

plotModule: Plot a specific module after running Spinglass algorithm

Description

This function is an adapted version of renderModule available through Epimods. We have added optional functionality including plotting the actual raw data onto the node edges, adding goseq annotation to the plot, legends and plotting modes.

Usage

plotModule(pvalue_annotation, p_thresh = 0.05, which_network = 1, goseq = FALSE, 
layout = "fr", legend = TRUE, namestyle = "symbol", suppress_details = FALSE, 
meth_hi_col = "blue", meth_low_col = "yellow1", 
meth_mid_col = "gray90", exp_hi_col = "red1", exp_low_col = "chartreuse1", 
exp_mid_col = "gray90", label_scale = TRUE, compare_plot=FALSE, 
pdf_out=NULL)

Arguments

pvalue_annotation

An S4 object of class PvalueAnnotation

p_thresh

A numeric specifying a threshold for plotting raw data on edges of nodes. DEFAULT is alpha=0.05. Items above this threshold will be classified as "mid" instead of "high" or "low" "

which_network

A numeric specifying which network to plot. DEFAULTS to 1, and will not plot another network until specified explicitly.

goseq

A logical indicating whether to plot goseq results for the module on the right hand side of the plot.

layout

A character string as either "fr" (DEFAULT) for fruchterman.reingold or "circle" for a circular plot.

legend

A logical (TRUE(DEFAULT)/FALSE) specifying whether a legend should be drawn.

namestyle

A character string as either "symbol" (DEFAULT) for gene symbols or "refseq" for RefSeq genes. If modules were performed on RefSeq genes, then the function will plot with gene symbols so that it is more useful.

suppress_details

A logical (TRUE(DEFAULT)/FALSE) indicating whether border raw data information should be plotted.

meth_hi_col

A color to be associated with signficant modification data with positive effects

meth_low_col

A color to be associated with signficant modification data with negative effects

meth_mid_col

A color to be associated with non-signficant modification data

exp_hi_col

A color to be associated with signficant expression data with postive effects

exp_low_col

A color to be associated with signficant expression data with negative effects

exp_mid_col

A color to be associated with non-signficant expression data

compare_plot

A logical (TRUE/FALSE(DEFAULT)) indicating whether two plots should be drawn side by side, one with raw data and one without

label_scale

A logical (TRUE/FALSE(DEFAULT)) indicating whether whether the node label should be scaled with the node score

pdf_out

A string indicating a location to which the function should output a pdf. If NULL (DEFAULT) then no pdf is made.

Value

A plot of the module

See Also

extractModules

Examples

data(test_annotation_score_data)

#plotModule(pvalue_annotation=test_annotation, which_network=2)

#plotModule(pvalue_annotation=test_annotation, which_network=2,
#suppressDetails=TRUE)