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Trying out RWikiPathways
Raw
Trying out RWikiPathways.Rmd
---
title: "Extract Nodes and Edges from Wiki Pathways"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rWikiPathways")
library(rWikiPathways)
```
# R Markdown - Extract Nodes and Edges from Wikipathways
## Using XML2 package - Example XML file
```{r}
library(xml2)
# Example simple XML file
x <- xml2::read_xml("<foo>
<bar>text <baz id = 'a' /></bar>
<bar>2</bar>
<baz id = 'b' />
</foo>")
xml_children(x)
baz <- xml_find_all(x, ".//baz") #works well
bar <- xml_find_all(x, ".//bar") #works well
```
## Using XML2 package - Read from GPML / wikipathways
```{r}
library(xml2)
gpml <- rWikiPathways::getPathway('WP1589')
x2 <- xml2::read_xml(gpml)
xml_children(x2) #lists all child nodes
x3 <- xml_children(x2) #69 chlid nodes - correct
#Find all DataNode tags
dataNode <- xml2::xml_find_all(x2, ".//DataNode") #not working
dataNode <- xml2::xml_find_all(x3, ".//DataNode") #not working
```
## Trying using XML package
```{r}
library(XML)
gpml <- rWikiPathways::getPathway('WP1589')
xml_data <- xmlToList(gpml) #list of 70
## extract list of of all DataNodes
namesXML <- (names(xml_data)=="DataNode")
xmlDataNode <- xml_data[namesXML] # 26 DataNodes
### Need to extract "DataNode" tags and collate into a dataframe,
#so that the nodes can be obtained
## Try 1 - unlist this into a data frame --- not correct
xmlDataNode2 <- data.frame(matrix(unlist(xmlDataNode),
ncol=15,
byrow=T))
## Try 2 - Using Biobase to extract sublist
BiocManager::install("Biobase")
library(Biobase)
newGraphics <- Biobase::subListExtract(xmlDataNode, "Graphics",
simplify = FALSE,
keep.names = TRUE)
newXREf <- Biobase::subListExtract(xmlDataNode, "Xref",
simplify = FALSE,
keep.names = TRUE)
newAttrs <- Biobase::subListExtract(xmlDataNode, ".attrs",
simplify = FALSE, keep.names = TRUE)
#apply Lapply to collate them --- not correct
newGraphics2 <- data.frame(lapply(newGraphics, "length<-",
max(lengths(newGraphics)))) #not correct
## Try 3 --- not correct
newGraphics2 <- sapply(newGraphics, '[', seq(max(sapply(newGraphics, length))))
```
# Try 4
```{r}
gpml <- rWikiPathways::getPathway('WP1589')
g1 <- XML::xmlParse(gpml)
# Exract the root node form the xml file.
rootnode <- xmlRoot(g1)
print(rootnode)
# Find number of nodes in the root.
rootsize <- xmlSize(rootnode)
dataNode <- rootnode[2]
xmldataframe <- xmlToDataFrame(gpml) #does not work
```
Raw
WP1589 GPML Pathway file
<?xml version="1.0" encoding="UTF-8"?>
<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Folate-Alcohol and Cancer Pathway Hypotheses" Organism="Homo sapiens" License="CC BY 2.0">
<Comment Source="WikiPathways-description">As described in Hwang, et al., "The interaction of folate and alcohol consumption has been shown to have an antagonistic effect on the risk of oral cancer. Studies have demonstrated that increased intake of folate decreases the risk of oral cancer, while greater alcohol consumption has an opposite effect." This pathway is a hypothetical model for a causal role for P450 2E1 (CYP2E1) and aldehyde dehydrogenase 1 (ALDH1) in oral cancers, implicating folate (via SAM) and alcohol.</Comment>
<Comment Source="WikiPathways-category">Cellular Process</Comment>
<BiopaxRef>b5e</BiopaxRef>
<Graphics BoardWidth="820.1596638655462" BoardHeight="581.470588235294" />
<DataNode TextLabel="Nucleotide Synthesis" GraphId="a9be0" Type="Pathway">
<Graphics CenterX="177.88655462184897" CenterY="119.98319327731093" Width="137.68907563025218" Height="20.0" ZOrder="32768" FontWeight="Bold" FontSize="12" Valign="Middle" ShapeType="None" Color="14961e" />
<Xref Database="WikiPathways" ID="WP404" />
</DataNode>
<DataNode TextLabel="ALDH1A1" GraphId="ad1b0" Type="GeneProduct">
<Graphics CenterX="674.04063397511" CenterY="352.13571842239054" Width="62.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="216" />
</DataNode>
<DataNode TextLabel="THF" GraphId="af2aa" Type="Metabolite">
<Graphics CenterX="303.7605042016813" CenterY="182.16806722689083" Width="35.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0033ff" />
<Xref Database="ChEBI" ID="CHEBI:20506" />
</DataNode>
<DataNode TextLabel="MTR" GraphId="b06ca" Type="GeneProduct">
<Graphics CenterX="409.3109243697479" CenterY="208.8487394957983" Width="48.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" />
<Xref Database="Ensembl" ID="ENSG00000116984" />
</DataNode>
<DataNode TextLabel="Cystathionine" GraphId="b149e" Type="Metabolite">
<Graphics CenterX="598.3697478991596" CenterY="136.1680672268907" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="HMDB" ID="HMDB0000099" />
</DataNode>
<DataNode TextLabel="Methionine" GraphId="b9d15" Type="Metabolite">
<Graphics CenterX="515.3697478991598" CenterY="231.16806722689105" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="HMDB" ID="HMDB0000696" />
</DataNode>
<DataNode TextLabel="SAM" GraphId="ba0c7" Type="Metabolite">
<Graphics CenterX="538.8697478991598" CenterY="277.16806722689114" Width="35.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0033ff" />
<Xref Database="Chemspider" ID="8041295" />
</DataNode>
<DataNode TextLabel="ALDH1A1" GraphId="bc141" Type="GeneProduct">
<Graphics CenterX="198.1598545044154" CenterY="466.1769586237407" Width="63.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="216" />
</DataNode>
<DataNode TextLabel="C/EBPB" GraphId="bfd2b" Type="GeneProduct">
<Graphics CenterX="232.15985450441494" CenterY="408.1769586237407" Width="59.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="1051" />
</DataNode>
<DataNode TextLabel="Acetaldehyde" GraphId="c5fba" Type="Metabolite">
<Graphics CenterX="612.0406339751103" CenterY="381.13571842239054" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="HMDB" ID="HMDB0000990" />
</DataNode>
<DataNode TextLabel="Acetate" GraphId="c683c" Type="Metabolite">
<Graphics CenterX="736.5406339751105" CenterY="381.13571842239054" Width="55.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="ChEBI" ID="CHEBI:30089" />
</DataNode>
<DataNode TextLabel="CYP2E1" GraphId="d0d43" Type="GeneProduct">
<Graphics CenterX="332.15985450441553" CenterY="382.80672268907654" Width="53.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="1571" />
</DataNode>
<DataNode TextLabel="SAH" GraphId="d3887" Type="Metabolite">
<Graphics CenterX="615.2447478991596" CenterY="222.91806722689105" Width="36.25" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0033ff" />
<Xref Database="ChEBI" ID="CHEBI:16680" />
</DataNode>
<DataNode TextLabel="Homocysteine" GraphId="d3cdc" Type="Metabolite">
<Graphics CenterX="527.3697478991598" CenterY="178.16806722689094" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="HMDB" ID="HMDB0000742" />
</DataNode>
<DataNode TextLabel="Folate" GraphId="da9e1" Type="Metabolite">
<Graphics CenterX="42.86554621848739" CenterY="297.5714285714288" Width="44.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="ChEBI" ID="CHEBI:62501" />
</DataNode>
<DataNode TextLabel="ADH5" GraphId="df139" Type="GeneProduct">
<Graphics CenterX="530.0406339751084" CenterY="410.13571842239054" Width="46.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Ensembl" ID="ENSG00000197894" />
</DataNode>
<DataNode TextLabel="CREB1" GraphId="e07a6" Type="GeneProduct">
<Graphics CenterX="231.78485450441494" CenterY="365.9269586237407" Width="45.75" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="1385" />
</DataNode>
<DataNode TextLabel="CYP2E1" GraphId="e3213" Type="GeneProduct">
<Graphics CenterX="530.5406339751084" CenterY="351.13571842239054" Width="53.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
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</DataNode>
<DataNode TextLabel="ALDH1L1" GraphId="e7315" Type="GeneProduct">
<Graphics CenterX="271.6598545044154" CenterY="465.1769586237407" Width="62.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
<Xref Database="Entrez Gene" ID="10840" />
</DataNode>
<DataNode TextLabel="MTHFR" GraphId="f0200" Type="GeneProduct">
<Graphics CenterX="150.7100840336133" CenterY="225.86554621848765" Width="51.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
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</DataNode>
<DataNode TextLabel="5,10-Methylene-THF" GraphId="f24f5" Type="Metabolite">
<Graphics CenterX="177.15966386554612" CenterY="181.1176470588236" Width="114.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
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</DataNode>
<DataNode TextLabel="Ethanol" GraphId="f6e34" Type="Metabolite">
<Graphics CenterX="455.26204958309296" CenterY="380.2282774060566" Width="52.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
<Xref Database="HMDB" ID="HMDB0000108" />
</DataNode>
<DataNode TextLabel="5-Methyl THF" GraphId="f9879" Type="Metabolite">
<Graphics CenterX="284.0168067226891" CenterY="237.0672268907566" Width="74.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
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<Graphics CenterX="714.7771889154938" CenterY="136.33503637389614" Width="59.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" Color="0000ff" />
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<DataNode TextLabel="CBS" GraphId="fd150" Type="GeneProduct">
<Graphics CenterX="512.3697478991598" CenterY="125.16806722689071" Width="42.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
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