packexplorer: Help in searching for new packages

Documented in who_are_you

#' Characterize a package neighborhood
#'
#' This function gives you an ego network of a package (the package and its surrounders).
#' @param pack The package of interest.
#' @param plot.it Should the network be plotted? Default is TRUE
#' @param return.map Should the network be returned? Default is FALSE
#' @param point.size The aspect of the packages giving their size. If 'score', their size is given based in their score. If 'downloads', their size is base in ther daily downloads. Else its the same for all of them. If you want to specify a size use min.point.size
#' @param add_my_packs Should your packages be added to the plot? Default is FALSE
#' @param my_packs_neighbors If add_my_packs is TRUE, should only keep the surrounders of pack? Default is FALSE
#' @param min.point.size The min point size, passed to leaflet. Default is 15
#' @param max.point.size The max point size, passed to leaflet. Default is 30
#' @param nwords The number of words per line in the package's description
#' @return A dataframe and also a plot.
#' @export
#' @examples
#' who_are_you('leaflet')
#' @importFrom igraph V neighbors induced_subgraph E %<-% as_ids layout_nicely head_of tail_of E<- V<-
#' @importFrom leaflet leaflet addCircleMarkers addPolylines addLegend addLabelOnlyMarkers labelOptions

who_are_you = function(pack,plot.it = TRUE,return.map = F,nwords=5,add_my_packs=FALSE,my_packs_neighbors=FALSE,point.size='downloads',min.point.size=15,max.point.size=30){
  available_packages = intersect(V(gd)$name,intersect(V(gs)$name,intersect(V(gi)$name,V(ge)$name)))
  if(!is.element(pack,available_packages)){
    return('Requested package is not available')  
  }
  desc = desc[is.element(desc$Package,V(gd)$name),]
	cats = cats[is.element(cats$Package,V(gd)$name),]
	downloads = downloads[is.element(downloads$Package,V(gd)$name),]
	pack_depends = neighbors(graph=gd,v=pack,mode='in')
	pack_revdepends = neighbors(graph=gd,v=pack,mode='out')
	pack_revsuggests = neighbors(graph=gs,v=pack,mode='out')
	pack_suggests = neighbors(graph=gs,v=pack,mode='in')
	pack_imports = neighbors(graph=gi,v=pack,mode='in')
	pack_revimports = neighbors(graph=gi,v=pack,mode='out')
	pack_revenhances = neighbors(graph=ge,v=pack,mode='out')
	pack_enhances = neighbors(graph=ge,v=pack,mode='in')
	gs_neighborhood = induced_subgraph(graph = gs, vids = c(pack,(igraph::union(pack_revsuggests,pack_suggests))$name))
	gd_neighborhood = induced_subgraph(graph = gd, vids = c(pack,(igraph::union(pack_depends,pack_revdepends))$name))
	ge_neighborhood = induced_subgraph(graph = ge, vids = c(pack,(igraph::union(pack_enhances,pack_revenhances))$name))
	gi_neighborhood = induced_subgraph(graph = gi, vids = c(pack,(igraph::union(pack_imports,pack_revimports))$name))
	packlist = c(pack,(igraph::union(pack_revsuggests,pack_suggests))$name,(igraph::union(pack_depends,pack_revdepends))$name,(igraph::union(pack_revimports,pack_imports))$name,(igraph::union(pack_enhances,pack_revenhances))$name)
	if(add_my_packs){
		my_packs = rownames(utils::installed.packages())
		if(my_packs_neighbors){
			g_full = igraph::union(gs,igraph::union(gd,igraph::union(gi,ge)))
			my_packs = intersect(my_packs,neighbors(graph=g_full,v=pack, mode = 'all'))
		}
		packlist = c(packlist,my_packs)
		packlist = intersect(packlist,union(V(gs)$name,V(gd)$name))
	}
	g = induced_subgraph(graph = igraph::union(igraph::union(igraph::union(gs,gd),gi),ge), vids = packlist)
	V(g)$color = 'black'
	V(g)$color[is.element(V(g)$name,V(gs_neighborhood)$name)] = 'red'
	V(g)$color[is.element(V(g)$name,V(gd_neighborhood)$name)] = 'blue'
	V(g)$color[is.element(V(g)$name,V(gi_neighborhood)$name)] = 'green'
	V(g)$color[is.element(V(g)$name,V(ge_neighborhood)$name)] = 'orange'
	V(g)$color[is.element(V(g)$name,V(gs_neighborhood)$name) & is.element(V(g)$name,V(gd_neighborhood)$name)] = 'violet'
	V(g)$color[is.element(V(g)$name,rownames(utils::installed.packages()))] = 'white'
	V(g)$color[is.element(V(g)$name,pack)] = 'black'
	Eg = as_ids(E(g))
	Egs = as_ids(E(gs_neighborhood))
	Egd = as_ids(E(gd_neighborhood))
	Egi = as_ids(E(gi_neighborhood))
	Ege = as_ids(E(ge_neighborhood))
	E(g)$color = 'gray'
	E(g)$color[is.element(Eg,Egs) & is.element(tail_of(graph = g, es = E(g))$name, pack)] = 'red'
	E(g)$color[is.element(Eg,Egs) & is.element(head_of(graph = g, es = E(g))$name, pack)] = 'orange'
	E(g)$color[is.element(Eg,Egd) & is.element(tail_of(graph = g, es = E(g))$name, pack)] = 'blue'
	E(g)$color[is.element(Eg,Egd) & is.element(head_of(graph = g, es = E(g))$name, pack)] = 'green'
	E(g)$color[is.element(Eg,Egi) & is.element(tail_of(graph = g, es = E(g))$name, pack)] = 'pink'
	E(g)$color[is.element(Eg,Egi) & is.element(head_of(graph = g, es = E(g))$name, pack)] = 'brown'
	E(g)$color[is.element(Eg,Ege) & is.element(tail_of(graph = g, es = E(g))$name, pack)] = 'yellow'
	E(g)$color[is.element(Eg,Ege) & is.element(head_of(graph = g, es = E(g))$name, pack)] = 'violet'
	output = list()
	output$igraph.graph = g
	l = scale(layout_nicely(g))
	listConnections = list_connections(graph = g,layout = l)
	labs = generate_labels(graph=g,nwords=nwords)

	if(point.size=='score'){
		g1 = V(g)$name
		g2 = row.names(utils::installed.packages())
		scores = number_of_connecting_edges(g,g1,g2)
		scores[is.element(names(scores),g2)]=0
		radii = min.point.size+(max.point.size-min.point.size)*as.numeric(ifelse(is.na(scores),0,scores)/max(c(scores,1),na.rm=T))
		labels = lapply(1:length(V(g)), function(i){paste(labs[[i]],' <p>','Score: ',scores[i],'</p>',sep='')})
		labels = lapply(labels, HTML)
	}else{
		if(point.size=='downloads'){
			desc.rate = downloads$Downloads[match(V(g)$name,as.character(downloads$Package))]
			radii = min.point.size + (max.point.size-min.point.size)*desc.rate/max(desc.rate,na.rm=T)
			radii[is.na(radii)] = min.point.size 
			labels = lapply(1:length(V(g)), function(i){paste(labs[[i]],' <p>','Downloads rate: ',round(desc.rate[i],3),'</p>',sep='')})
			labels = lapply(labels, HTML)
		}else{
			radii = min.point.size
			labels = lapply(labs, HTML)
		}
	}
	coloresMapV = c('black','white','red','blue','green','orange')
	labelsMapV = c(pack,'My packs','Via Suggests','Via Depends','Via Imports','Via Enhances')
	if(is.element('violet',V(g)$color)){
		coloresMapV = c(coloresMapV,'violet')
		labelsMapV = c(labelsMapV,'Via Suggests & Depends')
	}
	coloresMapE = c('red','orange','blue','green','pink','brown','yellow','violet','gray')
	labelsMapE = c(paste('suggests to',pack),paste(pack,'suggests to'),paste('deppends from',pack),paste(pack,'deppends from'),paste('imports',pack),paste(pack,'imports'),paste('enhances',pack),paste(pack,'enhances'),'other')
	map <- leaflet(data=l) %>% addPolylines(data=listConnections,lng=~x,lat = ~y,weight=2,color=E(g)$color) %>% addCircleMarkers(lng=l[,1],lat = l[,2],label=labels,color=V(g)$color,radius=radii,opacity=1,fillOpacity=1) %>%
	addLegend(colors=coloresMapV,labels=labelsMapV) %>% addLegend(colors=coloresMapE,labels=labelsMapE) %>%
	addLabelOnlyMarkers(lng=l[,1],lat = l[,2],label=V(g)$name,labelOptions=labelOptions(textsize='8px'))
	output$leaflet.graph = map
	if(plot.it){
		print(map)
	}
	if(return.map) return(output)
}