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Last data update: 2014.03.03

R: Export augmented pathways to pdf

pathways2pdf

R Documentation

Export augmented pathways to pdf

Description

This function creates a pdf file with plottings of a list of augmented pathways.

Usage

pathways2pdf(original_pathways, augmented_pathways, pathway_names, file)

Arguments

`original_pathways`	A list of graph::graphNEL objects where each of the nodes is named with '<gene_ID>'. Nodes of each graph::graphNEL represent the genes involved in the pathway and edges represent the biological interactions (activation or repression) among those genes (activation or repression).
`augmented_pathways`	A list of graph::graphNEL objects where each of the nodes is named with '<gene_ID>'. Nodes of each graph::graphNEL represent genes and miRNAs involved in the pathway and edges represent the biological interactions (activation or repression) among them.
`pathway_names`	A list of names of the pathways named by '<pathway_ID>'.
`file`	The name of the file where the plots will be saved.

Value

A pdf file with the plottings of the augmented pathways.

Author(s)

Diana Diaz <dmd at wayne dot edu>

Examples

data(augmented_pathways)
data(kegg_pathways)
data(names_pathways)
#The following instruction writes a pfd with three pathways
pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20],
             names_pathways[18:20], "three_pathways.pdf")
#The following instruction writes a pfd with all the pathways:
#NOTE: It may take time.
# pathways2pdf(kegg_pathways,augmented_pathways,
#              names_pathways, "all_pathways.pdf")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirIntegrator)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirIntegrator/pathways2pdf.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pathways2pdf
> ### Title: Export augmented pathways to pdf
> ### Aliases: pathways2pdf
> 
> ### ** Examples
> 
> data(augmented_pathways)
> data(kegg_pathways)
> data(names_pathways)
> #The following instruction writes a pfd with three pathways
> pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20],
+              names_pathways[18:20], "three_pathways.pdf")
Warning messages:
1: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor,  :
  zero-length arrow is of indeterminate angle and so skipped
2: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor,  :
  zero-length arrow is of indeterminate angle and so skipped
3: In par(opar) : graphical parameter "cin" cannot be set
4: In par(opar) : graphical parameter "cra" cannot be set
5: In par(opar) : graphical parameter "csi" cannot be set
6: In par(opar) : graphical parameter "cxy" cannot be set
7: In par(opar) : graphical parameter "din" cannot be set
8: In par(opar) : graphical parameter "page" cannot be set
> #The following instruction writes a pfd with all the pathways:
> #NOTE: It may take time.
> # pathways2pdf(kegg_pathways,augmented_pathways,
> #              names_pathways, "all_pathways.pdf")
> 
> 
> 
> 
> 
> dev.off()
Error in dev.off() : cannot shut down device 1 (the null device)
Execution halted