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R/xA2Net.r
In A2: Atlas and Analysis of Systems-Biology-Led Pathways
Defines functions
xA2Net
Documented in
xA2Net
#' Function to visualise an igraph object in a ggplot style
#'
#' \code{xA2Net} is supposed to visualise an igraph object in a ggplot style.
#'
#' @param g an object of class "igraph". For an advanced use, it can be a list of igraph objects; in this case, multiple panels will be shown (particularly useful when visualising the same network but color-coded differently)
#' @param node.label either a vector labelling nodes or a character specifying which node attribute used for the labelling. If NULL (by default), no node labelling
#' @param label.wrap.width a positive integer specifying wrap width of node labelling
#' @param label.wrap.lineheight line height spacing for text in ggplot. By default it is 0.8
#' @param node.label.size a character specifying which node attribute used for node label size
#' @param node.label.fontface a character specifying which node attribute used for node label fontface ('plain', 'bold', 'italic', 'bold.italic')
#' @param node.label.color a character specifying which node attribute used for the node label color
#' @param node.label.alpha the 0-1 value specifying transparency of node labelling
#' @param node.label.padding the padding around the labeled node
#' @param node.label.arrow the arrow pointing to the labeled node
#' @param node.label.force the repelling force between overlapping labels
#' @param node.shape an integer specifying node shape or a character specifying which node attribute used for the node shape (no matter whether it is numeric or character)
#' @param node.shape.title a character specifying the title for node shaping
#' @param node.xcoord a vector specifying x coordinates. If NULL, it will be created using igraph::layout_with_kk
#' @param node.ycoord a vector specifying y coordinates. If NULL, it will be created using igraph::layout_with_kk
#' @param node.color a character specifying which node attribute used for node coloring
#' @param node.color.title a character specifying the title for node coloring
#' @param 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 \url{http://html-color-codes.info/color-names}
#' @param ncolors the number of colors specified over the colormap
#' @param zlim the minimum and maximum values for which colors should be plotted
#' @param na.color the color for NAs. By default, it is 'grey80'
#' @param node.size either a vector specifying node size or a character specifying which node attribute used for the node size
#' @param node.size.title a character specifying the title for node sizing
#' @param node.size.range the range of actual node size
#' @param slim the minimum and maximum values for which sizes should be plotted
#' @param title a character specifying the title for the plot
#' @param edge.size a numeric value specifying the edge size. By default, it is 0.5
#' @param edge.color a character specifying which edge attribute defining the the edge colors
#' @param edge.color.alpha the 0-1 value specifying transparency of edge colors
#' @param edge.curve a numeric value specifying the edge curve. 0 for the straight line
#' @param edge.arrow a numeric value specifying the edge arrow. By default, it is 2
#' @param edge.arrow.gap a gap between the arrow and the node
#' @return
#' a ggplot object, appended with 'data_nodes' and 'data_edges'
#' @note none
#' @export
#' @seealso \code{\link{xA2Net}}
#' @include xA2Net.r
#' @examples
#' # Load the library
#' library(A2)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev/"
#'
#' \dontrun{
#' # load REACTOME
#' # restricted to Immune System ('R-HSA-168256') or Signal Transduction ('R-HSA-162582')
#' g <- xRDataLoader(RData.customised='ig.REACTOME', RData.location=RData.location)
#' neighs.out <- igraph::neighborhood(g, order=vcount(g), nodes="R-HSA-168256", mode="out")
#' nodeInduced <- V(g)[unique(unlist(neighs.out))]$name
#' ig <- igraph::induced.subgraph(g, vids=nodeInduced)
#'
#' # visualise the graph with vertices being color-coded
#' V(ig)$degree <- igraph::degree(ig)
#' gp <- xA2Net(g=ig, node.label='term_id', label.wrap.width=30, node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=1, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='degree', node.color.title='Degree', colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10), node.size.range=3, edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02, title='')
#' # advanced use: visualise the list of graphs
#' ls_ig <- list(ig, ig)
#' gp <- xA2Net(g=ls_ig, node.label='term_id', label.wrap.width=30, node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=1, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='degree', node.color.title='Degree', colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10), node.size.range=3, edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02, title='')
#'
#' ###########################
#' # visualise gene network
#' glayout <- igraph::layout_with_kk(g)
#' V(g)$xcoord <- glayout[,1]
#' V(g)$ycoord <- glayout[,2]
#' V(g)$degree <- igraph::degree(g)
#' gp <- xA2Net(g=g, node.label='name', node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=0.01, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority', node.color.title='5-star\nrating', colormap='yellow-red', ncolors=64, zlim=c(0,5), node.size='degree', node.size.title='Degree', slim=c(0,5), edge.color="orange",edge.color.alpha=0.5,edge.curve=0,edge.arrow.gap=0.025, title='')
#' gp_rating <- xA2Net(g=g, node.label='name', node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0.1, node.label.arrow=0, node.label.force=0.01, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority', node.color.title='5-star\nrating', colormap='white-yellow-red', ncolors=64, zlim=c(0,5), node.size.range=5, edge.color="orange",edge.color.alpha=0.3,edge.curve=0,edge.arrow.gap=0.02, title='')
#' }
xA2Net <- function(g, node.label=NULL, label.wrap.width=NULL, label.wrap.lineheight=0.8, node.label.size=NULL, node.label.fontface='plain', node.label.color='darkblue', node.label.alpha=0.8, node.label.padding=1, node.label.arrow=0.01, node.label.force=1, node.shape=19, node.shape.title=NULL, node.xcoord=NULL, node.ycoord=NULL, node.color=NULL, node.color.title=NULL, colormap='grey-orange-darkred', ncolors=64, zlim=NULL, na.color='grey80', node.size=NULL, node.size.title=NULL, node.size.range=c(1,4), slim=NULL, title='', edge.size=0.5, edge.color="black", edge.color.alpha=0.5, edge.curve=0.1, edge.arrow=2, edge.arrow.gap=0.02)
{
if(any(class(g) %in% c("igraph"))){
ls_ig <- list(g)
}else if(class(g)=="list"){
## Remove null elements in a list
ls_ig <- base::Filter(base::Negate(is.null), g)
if(length(ls_ig)==0){
return(NULL)
}
}else{
stop("The function must apply to 'list' of 'igraph' objects or a 'igraph' object.\n")
}
## check list_names
ls_names <- names(ls_ig)
if(is.null(ls_names)){
ls_names <- paste('IG', 1:length(ls_ig), sep='_')
names(ls_ig) <- ls_names
}
#################
gp <- XGR::xGGnetwork(g=ls_ig, node.label=node.label, label.wrap.width=label.wrap.width, label.wrap.lineheight=label.wrap.lineheight, node.label.size=node.label.size, node.label.fontface=node.label.fontface, node.label.color=node.label.color, node.label.alpha=node.label.alpha, node.label.padding=node.label.padding, node.label.arrow=node.label.arrow, node.label.force=node.label.force, node.shape=node.shape, node.shape.title=node.shape.title, node.xcoord=node.xcoord, node.ycoord=node.ycoord, node.color=node.color, node.color.title=node.color.title, colormap=colormap, ncolors=ncolors, zlim=zlim, na.color=na.color, node.size=node.size, node.size.title=node.size.title, node.size.range=node.size.range, slim=slim, title=title, edge.size=edge.size, edge.color=edge.color, edge.color.alpha=edge.color.alpha, edge.curve=edge.curve, edge.arrow=edge.arrow, edge.arrow.gap=0.02)
#################
invisible(gp)
}
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A2 documentation built on May 2, 2019, 5 p.m.
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Defines functions xA2Net
Documented in xA2Net
#' Function to visualise an igraph object in a ggplot style
#'
#' \code{xA2Net} is supposed to visualise an igraph object in a ggplot style.
#'
#' @param g an object of class "igraph". For an advanced use, it can be a list of igraph objects; in this case, multiple panels will be shown (particularly useful when visualising the same network but color-coded differently)
#' @param node.label either a vector labelling nodes or a character specifying which node attribute used for the labelling. If NULL (by default), no node labelling
#' @param label.wrap.width a positive integer specifying wrap width of node labelling
#' @param label.wrap.lineheight line height spacing for text in ggplot. By default it is 0.8
#' @param node.label.size a character specifying which node attribute used for node label size
#' @param node.label.fontface a character specifying which node attribute used for node label fontface ('plain', 'bold', 'italic', 'bold.italic')
#' @param node.label.color a character specifying which node attribute used for the node label color
#' @param node.label.alpha the 0-1 value specifying transparency of node labelling
#' @param node.label.padding the padding around the labeled node
#' @param node.label.arrow the arrow pointing to the labeled node
#' @param node.label.force the repelling force between overlapping labels
#' @param node.shape an integer specifying node shape or a character specifying which node attribute used for the node shape (no matter whether it is numeric or character)
#' @param node.shape.title a character specifying the title for node shaping
#' @param node.xcoord a vector specifying x coordinates. If NULL, it will be created using igraph::layout_with_kk
#' @param node.ycoord a vector specifying y coordinates. If NULL, it will be created using igraph::layout_with_kk
#' @param node.color a character specifying which node attribute used for node coloring
#' @param node.color.title a character specifying the title for node coloring
#' @param 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 \url{http://html-color-codes.info/color-names}
#' @param ncolors the number of colors specified over the colormap
#' @param zlim the minimum and maximum values for which colors should be plotted
#' @param na.color the color for NAs. By default, it is 'grey80'
#' @param node.size either a vector specifying node size or a character specifying which node attribute used for the node size
#' @param node.size.title a character specifying the title for node sizing
#' @param node.size.range the range of actual node size
#' @param slim the minimum and maximum values for which sizes should be plotted
#' @param title a character specifying the title for the plot
#' @param edge.size a numeric value specifying the edge size. By default, it is 0.5
#' @param edge.color a character specifying which edge attribute defining the the edge colors
#' @param edge.color.alpha the 0-1 value specifying transparency of edge colors
#' @param edge.curve a numeric value specifying the edge curve. 0 for the straight line
#' @param edge.arrow a numeric value specifying the edge arrow. By default, it is 2
#' @param edge.arrow.gap a gap between the arrow and the node
#' @return
#' a ggplot object, appended with 'data_nodes' and 'data_edges'
#' @note none
#' @export
#' @seealso \code{\link{xA2Net}}
#' @include xA2Net.r
#' @examples
#' # Load the library
#' library(A2)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev/"
#'
#' \dontrun{
#' # load REACTOME
#' # restricted to Immune System ('R-HSA-168256') or Signal Transduction ('R-HSA-162582')
#' g <- xRDataLoader(RData.customised='ig.REACTOME', RData.location=RData.location)
#' neighs.out <- igraph::neighborhood(g, order=vcount(g), nodes="R-HSA-168256", mode="out")
#' nodeInduced <- V(g)[unique(unlist(neighs.out))]$name
#' ig <- igraph::induced.subgraph(g, vids=nodeInduced)
#'
#' # visualise the graph with vertices being color-coded
#' V(ig)$degree <- igraph::degree(ig)
#' gp <- xA2Net(g=ig, node.label='term_id', label.wrap.width=30, node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=1, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='degree', node.color.title='Degree', colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10), node.size.range=3, edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02, title='')
#' # advanced use: visualise the list of graphs
#' ls_ig <- list(ig, ig)
#' gp <- xA2Net(g=ls_ig, node.label='term_id', label.wrap.width=30, node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=1, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='degree', node.color.title='Degree', colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10), node.size.range=3, edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02, title='')
#'
#' ###########################
#' # visualise gene network
#' glayout <- igraph::layout_with_kk(g)
#' V(g)$xcoord <- glayout[,1]
#' V(g)$ycoord <- glayout[,2]
#' V(g)$degree <- igraph::degree(g)
#' gp <- xA2Net(g=g, node.label='name', node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0, node.label.arrow=0, node.label.force=0.01, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority', node.color.title='5-star\nrating', colormap='yellow-red', ncolors=64, zlim=c(0,5), node.size='degree', node.size.title='Degree', slim=c(0,5), edge.color="orange",edge.color.alpha=0.5,edge.curve=0,edge.arrow.gap=0.025, title='')
#' gp_rating <- xA2Net(g=g, node.label='name', node.label.size=2, node.label.color='black', node.label.alpha=0.8, node.label.padding=0.1, node.label.arrow=0, node.label.force=0.01, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority', node.color.title='5-star\nrating', colormap='white-yellow-red', ncolors=64, zlim=c(0,5), node.size.range=5, edge.color="orange",edge.color.alpha=0.3,edge.curve=0,edge.arrow.gap=0.02, title='')
#' }
xA2Net <- function(g, node.label=NULL, label.wrap.width=NULL, label.wrap.lineheight=0.8, node.label.size=NULL, node.label.fontface='plain', node.label.color='darkblue', node.label.alpha=0.8, node.label.padding=1, node.label.arrow=0.01, node.label.force=1, node.shape=19, node.shape.title=NULL, node.xcoord=NULL, node.ycoord=NULL, node.color=NULL, node.color.title=NULL, colormap='grey-orange-darkred', ncolors=64, zlim=NULL, na.color='grey80', node.size=NULL, node.size.title=NULL, node.size.range=c(1,4), slim=NULL, title='', edge.size=0.5, edge.color="black", edge.color.alpha=0.5, edge.curve=0.1, edge.arrow=2, edge.arrow.gap=0.02)
{
if(any(class(g) %in% c("igraph"))){
ls_ig <- list(g)
}else if(class(g)=="list"){
## Remove null elements in a list
ls_ig <- base::Filter(base::Negate(is.null), g)
if(length(ls_ig)==0){
return(NULL)
}
}else{
stop("The function must apply to 'list' of 'igraph' objects or a 'igraph' object.\n")
}
## check list_names
ls_names <- names(ls_ig)
if(is.null(ls_names)){
ls_names <- paste('IG', 1:length(ls_ig), sep='_')
names(ls_ig) <- ls_names
}
#################
gp <- XGR::xGGnetwork(g=ls_ig, node.label=node.label, label.wrap.width=label.wrap.width, label.wrap.lineheight=label.wrap.lineheight, node.label.size=node.label.size, node.label.fontface=node.label.fontface, node.label.color=node.label.color, node.label.alpha=node.label.alpha, node.label.padding=node.label.padding, node.label.arrow=node.label.arrow, node.label.force=node.label.force, node.shape=node.shape, node.shape.title=node.shape.title, node.xcoord=node.xcoord, node.ycoord=node.ycoord, node.color=node.color, node.color.title=node.color.title, colormap=colormap, ncolors=ncolors, zlim=zlim, na.color=na.color, node.size=node.size, node.size.title=node.size.title, node.size.range=node.size.range, slim=slim, title=title, edge.size=edge.size, edge.color=edge.color, edge.color.alpha=edge.color.alpha, edge.curve=edge.curve, edge.arrow=edge.arrow, edge.arrow.gap=0.02)
#################
invisible(gp)
}
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