plotModule: Plot a specific module after running Spinglass algorithm

In AJEinstein/SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

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, label_shadow = FALSE, 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(DEFAULT)/FALSE) indicating whether whether the node label should be scaled with the node score
label_shadow	A logical (TRUE/FALSE(DEFAULT)) indicating whether whether the node label should have a white text shadow for easier label reading
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

Author(s)

N. Ari Wijetunga

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)

AJEinstein/SMITE documentation built on Oct. 23, 2021, 7:44 a.m.