XGR (version 1.1.5)

xGraphML2AA: Function to generate a graphml file from a pathway upon query

Description

xGraphML2AA is supposed to generate a graphml file from a pathway upon query. If data is provided, pathway gene members are color-coded.

Usage

xGraphML2AA(data = NULL, org = c("human", "mouse"),
query = "AA:hsa04672", curation = c("manual", "automatic", "any"),
node.label = "label", node.color = "lfc",
colormap = "deepskyblue-lightyellow-darkorange", ncolors = 64,
nlegend = 9, zlim = NULL, legend.title = "",
title.thispath = NULL, node.tooltip = "tooltip",
node.highlight = "fdr", node.highlight.cutoff = 0.05,
edge.color = "#00000033", edge.width = 1, color.gene = "#dddddd",
color.thispath = "#dddddd", color.otherpath = "#eeeeee",
size.gene = 10, size.gene.found = 11, size.gene.highlight = 12,
filename = "xGraphML2AA", verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

data

a data frame

org

a character specifying an organism. Currently supported organisms are 'human' and 'mouse'

query

the identity of a pathway in query. The full list of pathways can be found at http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=hsa for human and at http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=mmu for mouse. For example, 'AA:hsa04672' for 'NOD-like receptor signaling pathway', where the prefix 'AA:' can be ignored. Alternatively, it can be key words describing the pathway

curation

the type of curation. It can be one of "manual" (the manual one 'AA' followed by the semi-manual one 'AT'), "automatic" (only the automatic one) or "any" (first the manual one then the automatic one)

node.label

a character specifying which column used for node labelling. By default, it is 'label'

node.color

a character specifying which column used for node coloring. By default, it is 'lfc'

colormap

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

ncolors

the number of colors specified over the colormap

nlegend

the number of colors specified in the legend. By default, it is 11

zlim

the minimum and maximum z/patttern values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted

legend.title

the legend title. By default, it is ''

title.thispath

the appended title for this pathway. By default, it is NULL

node.tooltip

a character specifying which column used for node tooltip. By default, it is 'tooltip'. If not found, it will be 'Symbol-Name-Color'

node.highlight

a character specifying which column used for node highlighting. By default, it is 'fdr'. If so, those highlighted will have bold and larger labels

node.highlight.cutoff

a numeric specifying the cutoff for node highlighting. By default, it is 0.05 meaninght those less than this cutoff will be highlighted

edge.color

a character specifying the edge colors. By default, it is '#00000033'

edge.width

the edge width. By default, it is 1

color.gene

a character specifying the gene node colors. By default, it is '#dddddd'

color.thispath

a character specifying the color for this pathway node. By default, it is '#dddddd'

color.otherpath

a character specifying the color for other pathway nodes. By default, it is '#eeeeee'

size.gene

an integer character specifying the gene label fontsize. By default, it is 10

size.gene.found

an integer character specifying the label fontsize for genes found/matched. By default, it is 11

size.gene.highlight

an integer character specifying the label fontsize for genes highlighted. By default, it is 12

filename

the without-extension part of the name of the output file. By default, it is 'xGraphML2AA'

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

invisible (a string storing graphml-formatted content). If the filename is not NULL, a graphml-formatted file is also output.

See Also

xGraphML2AA

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

# }
# NOT RUN {
data(Haploid_regulators)
## IRF1 regulators
data <- subset(Haploid_regulators, Phenotype=='IRF1')

xGraphML2AA(query="AA:hsa04630", RData.location=RData.location,
color.gene='#dde8f1',size.gene=11)

## load GWAS genes
GWAS_Gene <- xRDataLoader(RData.customised='GWAS_Gene',
RData.location=RData.location)
data <- GWAS_Gene %>% dplyr::filter(Odds_Ratio!='NULL' &
Disease_ID=='RA') %>% dplyr::transmute(label=Symbol,
lfc=log2(as.numeric(Odds_Ratio)), fdr=Pvalue) %>%
dplyr::group_by(label) %>% dplyr::summarise(lfc=max(lfc),
fdr=min(fdr))

## manual one (the same as curation='any')
xGraphML2AA(data, query="AA:hsa04630", curation='manual',
node.label="label", node.color="lfc", node.highlight='fdr',
node.highlight.cutoff=5e-8, filename='xGraphML2AA',
legend.title='log2(Odds ratio)', zlim=c(-1,1),
RData.location=RData.location)
## automatic one
xGraphML2AA(data, query="AA:hsa04630", curation='automatic',
node.label="label", node.color="lfc", node.highlight='fdr',
node.highlight.cutoff=5e-8, filename='xGraphML2AA',
legend.title='log2(Odds ratio)', zlim=c(-1,1),
RData.location=RData.location)

## key words 
xGraphML2AA(data, query="Asthma", curation='any', node.label="label",
node.color="lfc", node.highlight='fdr', node.highlight.cutoff=5e-8,
filename='xGraphML2AA', RData.location=RData.location,
legend.title='log2(Odds ratio)', zlim=c(-1,1))
# }