R/matrix_graph.R
In jgalgarra/kcorebip: Bipartite networks kcore decomposition and visualization
Defines functions
matrix_graph
Documented in
matrix_graph
library(reshape2)
#' Plotting a matrix graph
#'
#' This function plots the matrix graph of a bipartite network. Configuration parameters and
#' results are stored in a global environment called mat. This environment is not destroyed
#' after the function is executed, so the developer can store it in a configuration file, retrieve
#'
#' @param datadir the name of the file of the interaction matrix
#' @param filename the file with the interaction matrix
#' @param sep data file separator character
#' @param speciesinheader species names included as header and row names
#' @param orderby sets order of nodes, by kradius, kdegree or degree
#' @param label_strguilda string labels of guild a
#' @param label_strguildb string labels of guild b
#' @param label_size base label size
#' @param color_guild_a default filling for nodes of guild_a
#' @param color_guild_b default filling for nodes of guild_b
#' @param color_links color of matrix interactions
#' @param flip_matrix to switch row/column guilds,
#' @param links_weight show links weight as a gradient of color for weighted networks
#' @param show_species_names add species name to number,
#' @param show_title show network name as plot title,
#' @param show_legend show guilds legend,
#' @param print_to_file print plot to file,
#' @param plotsdir default print directory
#' @param plot_size in inches for printed plot,
#' @param ppi dots per inch
#' @param progress for interactive visualization
#' @export
matrix_graph <-function(datadir,filename,sep=",",speciesinheader=TRUE,
style="matrix",
orderby = "kradius",
label_strguilda = "Plant",
label_strguildb = "Pollinator",
label_size = 15,
color_guild_a = "#4169E1",
color_guild_b = "#FF1808",
color_links = 'grey7',
flip_matrix = FALSE,
links_weight = FALSE,
show_species_names = TRUE,
show_title = TRUE, show_legend = TRUE,
print_to_file = FALSE, plotsdir ="plot_results/",
plot_size = 8,
ppi = 300,
progress = NULL
)
{
plot_m <- function(longData,flip_matrix=FALSE,nname="",ncolor="green",links_weight=FALSE,
strA="",strB="",colorA="blue",colorB="red",lsize=8,show_title=TRUE,
show_legend=TRUE)
{
legends_text <- paste0(
"</span><span style = 'color:white'> </span><span style = 'text-align: center; padding-right: 20px; color:",colorA,"'>",paste('# ',strA,' '),
"</span><span style = 'color:white'>...</span><span style = 'text-align: right; margin-left:10px; color:",colorB,"'>",paste('#',strB),"</span>")
if (!flip_matrix){
if (!links_weight)
mplots<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=as.factor(value)))
else
mplots<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=(value+1)))
}
else{
if (!links_weight)
mplots<- ggplot(longData, aes(x = rev(speciesB), y = rev(speciesA),fill=as.factor(value)))
else
mplots<- ggplot(longData, aes(x = rev(speciesB), y = rev(speciesA),fill=(value+1)))
}
if (!links_weight)
mplots <- mplots + geom_tile(color = ncolor,alpha=1) + scale_fill_manual(values=c("white",ncolor))
else
mplots <- mplots+geom_tile(color = ncolor,)+scale_fill_continuous(type = "gradient", trans = "log",
low = "white", high = ncolor,
breaks = round)
mplots <- mplots + ylab("")+xlab("")+coord_fixed()
if (!flip_matrix){
mplots <- mplots +scale_x_discrete(position="top",labels=unique(longData$numA))+
scale_y_discrete(labels=unique(longData$numB))
} else {
mplots <- mplots +scale_x_discrete(position="top",labels=rev(unique(longData$numB)))+
scale_y_discrete(labels=rev(unique(longData$numA)))
}
if (links_weight)
lposition = "right"
else
lposition = "none"
if (show_legend)
mplots <- mplots+labs(caption=legends_text)
if (show_title)
mplots <- mplots+ggtitle(paste("Network:",mat$network_name))
angulo <- ifelse(show_species_names,90,0)
mplots <- mplots + theme_void()+theme(legend.position=lposition,
legend.title=element_blank(),
legend.text = element_text(size = lsize),
legend.key.size = unit(0.3, 'cm'),
axis.text.x = element_text(size=lsize,hjust=ifelse(show_species_names,0,0.5),vjust=ifelse(show_species_names,0.5,0),
angle=angulo,color=ifelse(!flip_matrix,colorA,colorB)),
axis.text.y = element_text(size = lsize,hjust=1,vjust=0.5,color=ifelse(!flip_matrix,colorB,colorA)),
plot.title = element_text(size=lsize+3,hjust=0.5),
axis.title.x=element_text(size=18,face="bold",color="grey40",
hjust=0.5),
plot.subtitle = ggtext::element_markdown(hjust=0,vjust=0),
plot.margin = unit(c(0.1,0.1,0.1,0.1), "cm"),
plot.caption = ggtext::element_markdown(size=lsize*1.2,hjust=1,vjust=0))
return(mplots)
}
create_labels <- function(M,nums,i,vnames,show_species=FALSE,flip_matrix=TRUE,guild="A"){
if (guild=="A")
mn <- vnames[which(vnames$name==colnames(M)[i]),]$num
else
mn <- vnames[which(vnames$name==rownames(M)[i]),]$num
if (!flip_matrix){
if (guild=="A")
label <- (paste0(" ",mn," ",ifelse(show_species,colnames(M)[i],"")," "))
else
label <- (paste0(" ",mn," ",ifelse(show_species,paste0(rownames(M)[i],""),"")," "))
} else {
if (guild=="A")
label <- (paste0(" ",mn," ",ifelse(show_species,colnames(M)[i],"")," "))
else
label <- (paste0(" ",mn," ",ifelse(show_species,paste0(rownames(M)[i]," ")," ")))
}
label <- gsub("\\."," ",label)
return(label)
}
setkradiusorder <- function(dnodes){
myord <- rev(order(10000*dnodes$kshell-(100*dnodes$kradius-dnodes$kdegree+0.001*dnodes$num)))
return(dnodes$num[myord])
}
setkdegreeorder <- function(dnodes){
myord <- rev(order(100*dnodes$kdegree-dnodes$kradius))
return(dnodes$num[myord])
}
setdegreeorder <- function(dnodes){
myord <- rev(order(100*dnodes$degree-dnodes$kradius))
return(dnodes$num[myord])
}
mat_argg <- c(as.list(environment()))
# Analyze network
f <- kcorebip:::read_and_analyze(datadir,filename,label_strguilda, label_strguildb, sep = mat_argg$sep, speciesinheader = mat_argg$speciesinheader )
mat <<- new.env()
mat$result_analysis <- f["result_analysis"][[1]]
mat$str_guild_a <- f["str_guild_a"][[1]]
mat$str_guild_b <- f["str_guild_b"][[1]]
mat$name_guild_a <- f["name_guild_a"][[1]]
mat$name_guild_b <- f["name_guild_b"][[1]]
mat$network_name <- f["network_name"][[1]]
mat$mat_argg <- mat_argg
lnodes <- V(mat$result_analysis$graph)
species_a <- data.frame("num"=seq(1:mat$result_analysis$num_guild_a),"name"=colnames(mat$result_analysis$matrix))
species_a$kdegree <- lnodes$kdegree[1:mat$result_analysis$num_guild_a]
species_a$kradius <- lnodes$kradius[1:mat$result_analysis$num_guild_a]
if (sum(species_a$kradius==Inf)>0)
species_a[species_a$kradius==Inf,]$kradius=100
species_a$kshell <- lnodes$kcorenum[1:mat$result_analysis$num_guild_a]
species_a$num <- seq(1:mat$result_analysis$num_guild_a)
species_b <- data.frame("num"=seq(1:mat$result_analysis$num_guild_b),"name"=rownames(mat$result_analysis$matrix))
species_b$kdegree <- lnodes$kdegree[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
species_b$kradius <- lnodes$kradius[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
if (sum(species_b$kradius==Inf)>0)
species_b[species_b$kradius==Inf,]$kradius=100
species_b$kshell <- lnodes$kcorenum[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
species_b$num <- seq(1:mat$result_analysis$num_guild_b)
numberA <- mat$result_analysis$num_guild_a
numberB <- mat$result_analysis$num_guild_b
num_species <- numberA+numberB
M<-mat$result_analysis$matrix
binary_network = (sum(M>1)==0)
mat$binary_network <- binary_network
if(!is.null(progress))
mat$network_type <- ifelse(mat$binary_network,strings$value("LABEL_ZIGGURAT_INFO_BINARY"),strings$value("LABEL_ZIGGURAT_INFO_WEIGHTED"))
DegM <- M
DegM[DegM>1] <- 1
species_a$degree <- colSums(DegM)
species_b$degree <- rowSums(DegM)
# Vector that stores the node display order
if (orderby == "kradius"){
ordvectorA <- setkradiusorder(species_a)
ordvectorB <- rev(setkradiusorder(species_b))
}
if (orderby == "kdegree"){
ordvectorA <- setkdegreeorder(species_a)
ordvectorB <- rev(setkdegreeorder(species_b))
}
if (orderby == "degree"){
ordvectorA <- setdegreeorder(species_a)
ordvectorB <- rev(setdegreeorder(species_b))
}
species_a <- species_a[ordvectorA,]
species_b <- species_b[ordvectorB,]
if (!links_weight)
M[M>1]=1
M<-M[ordvectorB,ordvectorA]
num_b = species_b$num
num_a = species_a$num
longData<-melt(M)
mplots<- ggplot(longData, aes(x = Var2, y = Var1,fill=as.factor(value)))+geom_tile(alpha=1) + scale_fill_manual(values=c("white","red"))
longData$numA <- 0
longData$numB <- 0
names(longData) = c("speciesB","speciesA", "value","numB","numA")
mplots2<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=as.factor(value)))+geom_tile(alpha=1) + scale_fill_manual(values=c("white","blue"))
for (i in 1:length(colnames(M)))
longData[longData$speciesA==colnames(M)[i],]$numA = create_labels(M,num_a,i,species_a,show_species=show_species_names,flip_matrix=flip_matrix,guild="A")
for (i in 1:length(rownames(M)))
longData[longData$speciesB==rownames(M)[i],]$numB = create_labels(M,num_b,i,species_b,show_species=show_species_names,flip_matrix=flip_matrix,guild="B")
lsize <- label_size
if (!show_species_names)
lsize <- lsize*1.2
lsizeantes <- lsize
maxnum <- max(numberA,numberB)
minnum <- min(numberA,numberB)
if ((maxnum+minnum)<40)
lsize <-lsize/2
else {
lsize <- lsize * (1-(0.0025 *(150-min(140,maxnum)))) * (maxnum+minnum)/(2*maxnum)
lsize <- lsize * (1-(nchar(max(species_a$name,species_b$name))/50)^3)
lsize <- min(lsize,ifelse((maxnum+minnum)>100,0.66,1)*lsizeantes/2)
}
if (numberA < numberB){
myflip_matrix <- !flip_matrix
mat$landscape <- !flip_matrix
} else {
mat$landscape <- !flip_matrix
myflip_matrix <- flip_matrix
}
p <- plot_m(longData,flip_matrix=myflip_matrix,nname=mat$network_name,
strA=mat$name_guild_a,strB=mat$name_guild_b,
links_weight = (links_weight && !binary_network),
colorA=color_guild_a,colorB=color_guild_b,lsize=lsize,
ncolor=color_links,show_title = show_title,
show_legend=show_legend)
plsize = plot_size
dppi = ppi
if (show_species_names)
aspect = (nrow(species_a)+10)/(nrow(species_b)+10)
else
aspect = (nrow(species_a)+1)/(nrow(species_b)+1)
imw <- plsize*dppi
imh <- plsize*dppi/aspect
if (mat$landscape){
plot_width <- max(imw,imh)
plot_height <- min(imw,imh)
} else {
plot_width <- min(imw,imh)
plot_height <- max(imw,imh)
}
if (print_to_file){
dir.create(mat$mat_argg$plotsdir, showWarnings = FALSE)
nfile <- paste0(plotsdir,mat$network_name,"_MATRIX_orderby_",orderby,".png")
png(nfile,width=plot_width,height=plot_height,res=dppi)
print(p)
dev.off()
}
if (!is.null(progress)){
ppi = 300
dir.create("www", showWarnings = FALSE)
dir.create("www/reports/", showWarnings = FALSE)
nfile <- paste0("www/reports/",mat$network_name,"_MATRIX.png")
if (mat$landscape){
plot_width <- max(imw,imh)
plot_height <- min(imw,imh)
}
else{
plot_width <- min(imw,imh)
plot_height <- max(imw,imh)
}
png(nfile,width=plot_width,height=plot_height,res=dppi)
print(p)
dev.off()
mat$matrix_file <- nfile
}
mat$aspect <- aspect
mat$plot <- p
mat$flip_results <- flip_matrix
mat$plot_width <- plot_width * dppi #= plsize
mat$plot_height <- plot_height * dppi #plsize/aspect
return(mat)
}
debugging = FALSE
if (debugging)
p <- matrix_graph("../data/","dattilo2014.csv",
print_to_file = TRUE, plotsdir ="plot_results/",
orderby = "kradius",ppi=300,
flip_matrix = FALSE, links_weight = FALSE,
show_species_names = TRUE,
show_title = TRUE,
show_legend = TRUE)
jgalgarra/kcorebip documentation built on June 14, 2025, 12:33 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions matrix_graph
Documented in matrix_graph
library(reshape2)
#' Plotting a matrix graph
#'
#' This function plots the matrix graph of a bipartite network. Configuration parameters and
#' results are stored in a global environment called mat. This environment is not destroyed
#' after the function is executed, so the developer can store it in a configuration file, retrieve
#'
#' @param datadir the name of the file of the interaction matrix
#' @param filename the file with the interaction matrix
#' @param sep data file separator character
#' @param speciesinheader species names included as header and row names
#' @param orderby sets order of nodes, by kradius, kdegree or degree
#' @param label_strguilda string labels of guild a
#' @param label_strguildb string labels of guild b
#' @param label_size base label size
#' @param color_guild_a default filling for nodes of guild_a
#' @param color_guild_b default filling for nodes of guild_b
#' @param color_links color of matrix interactions
#' @param flip_matrix to switch row/column guilds,
#' @param links_weight show links weight as a gradient of color for weighted networks
#' @param show_species_names add species name to number,
#' @param show_title show network name as plot title,
#' @param show_legend show guilds legend,
#' @param print_to_file print plot to file,
#' @param plotsdir default print directory
#' @param plot_size in inches for printed plot,
#' @param ppi dots per inch
#' @param progress for interactive visualization
#' @export
matrix_graph <-function(datadir,filename,sep=",",speciesinheader=TRUE,
style="matrix",
orderby = "kradius",
label_strguilda = "Plant",
label_strguildb = "Pollinator",
label_size = 15,
color_guild_a = "#4169E1",
color_guild_b = "#FF1808",
color_links = 'grey7',
flip_matrix = FALSE,
links_weight = FALSE,
show_species_names = TRUE,
show_title = TRUE, show_legend = TRUE,
print_to_file = FALSE, plotsdir ="plot_results/",
plot_size = 8,
ppi = 300,
progress = NULL
)
{
plot_m <- function(longData,flip_matrix=FALSE,nname="",ncolor="green",links_weight=FALSE,
strA="",strB="",colorA="blue",colorB="red",lsize=8,show_title=TRUE,
show_legend=TRUE)
{
legends_text <- paste0(
"</span><span style = 'color:white'> </span><span style = 'text-align: center; padding-right: 20px; color:",colorA,"'>",paste('# ',strA,' '),
"</span><span style = 'color:white'>...</span><span style = 'text-align: right; margin-left:10px; color:",colorB,"'>",paste('#',strB),"</span>")
if (!flip_matrix){
if (!links_weight)
mplots<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=as.factor(value)))
else
mplots<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=(value+1)))
}
else{
if (!links_weight)
mplots<- ggplot(longData, aes(x = rev(speciesB), y = rev(speciesA),fill=as.factor(value)))
else
mplots<- ggplot(longData, aes(x = rev(speciesB), y = rev(speciesA),fill=(value+1)))
}
if (!links_weight)
mplots <- mplots + geom_tile(color = ncolor,alpha=1) + scale_fill_manual(values=c("white",ncolor))
else
mplots <- mplots+geom_tile(color = ncolor,)+scale_fill_continuous(type = "gradient", trans = "log",
low = "white", high = ncolor,
breaks = round)
mplots <- mplots + ylab("")+xlab("")+coord_fixed()
if (!flip_matrix){
mplots <- mplots +scale_x_discrete(position="top",labels=unique(longData$numA))+
scale_y_discrete(labels=unique(longData$numB))
} else {
mplots <- mplots +scale_x_discrete(position="top",labels=rev(unique(longData$numB)))+
scale_y_discrete(labels=rev(unique(longData$numA)))
}
if (links_weight)
lposition = "right"
else
lposition = "none"
if (show_legend)
mplots <- mplots+labs(caption=legends_text)
if (show_title)
mplots <- mplots+ggtitle(paste("Network:",mat$network_name))
angulo <- ifelse(show_species_names,90,0)
mplots <- mplots + theme_void()+theme(legend.position=lposition,
legend.title=element_blank(),
legend.text = element_text(size = lsize),
legend.key.size = unit(0.3, 'cm'),
axis.text.x = element_text(size=lsize,hjust=ifelse(show_species_names,0,0.5),vjust=ifelse(show_species_names,0.5,0),
angle=angulo,color=ifelse(!flip_matrix,colorA,colorB)),
axis.text.y = element_text(size = lsize,hjust=1,vjust=0.5,color=ifelse(!flip_matrix,colorB,colorA)),
plot.title = element_text(size=lsize+3,hjust=0.5),
axis.title.x=element_text(size=18,face="bold",color="grey40",
hjust=0.5),
plot.subtitle = ggtext::element_markdown(hjust=0,vjust=0),
plot.margin = unit(c(0.1,0.1,0.1,0.1), "cm"),
plot.caption = ggtext::element_markdown(size=lsize*1.2,hjust=1,vjust=0))
return(mplots)
}
create_labels <- function(M,nums,i,vnames,show_species=FALSE,flip_matrix=TRUE,guild="A"){
if (guild=="A")
mn <- vnames[which(vnames$name==colnames(M)[i]),]$num
else
mn <- vnames[which(vnames$name==rownames(M)[i]),]$num
if (!flip_matrix){
if (guild=="A")
label <- (paste0(" ",mn," ",ifelse(show_species,colnames(M)[i],"")," "))
else
label <- (paste0(" ",mn," ",ifelse(show_species,paste0(rownames(M)[i],""),"")," "))
} else {
if (guild=="A")
label <- (paste0(" ",mn," ",ifelse(show_species,colnames(M)[i],"")," "))
else
label <- (paste0(" ",mn," ",ifelse(show_species,paste0(rownames(M)[i]," ")," ")))
}
label <- gsub("\\."," ",label)
return(label)
}
setkradiusorder <- function(dnodes){
myord <- rev(order(10000*dnodes$kshell-(100*dnodes$kradius-dnodes$kdegree+0.001*dnodes$num)))
return(dnodes$num[myord])
}
setkdegreeorder <- function(dnodes){
myord <- rev(order(100*dnodes$kdegree-dnodes$kradius))
return(dnodes$num[myord])
}
setdegreeorder <- function(dnodes){
myord <- rev(order(100*dnodes$degree-dnodes$kradius))
return(dnodes$num[myord])
}
mat_argg <- c(as.list(environment()))
# Analyze network
f <- kcorebip:::read_and_analyze(datadir,filename,label_strguilda, label_strguildb, sep = mat_argg$sep, speciesinheader = mat_argg$speciesinheader )
mat <<- new.env()
mat$result_analysis <- f["result_analysis"][[1]]
mat$str_guild_a <- f["str_guild_a"][[1]]
mat$str_guild_b <- f["str_guild_b"][[1]]
mat$name_guild_a <- f["name_guild_a"][[1]]
mat$name_guild_b <- f["name_guild_b"][[1]]
mat$network_name <- f["network_name"][[1]]
mat$mat_argg <- mat_argg
lnodes <- V(mat$result_analysis$graph)
species_a <- data.frame("num"=seq(1:mat$result_analysis$num_guild_a),"name"=colnames(mat$result_analysis$matrix))
species_a$kdegree <- lnodes$kdegree[1:mat$result_analysis$num_guild_a]
species_a$kradius <- lnodes$kradius[1:mat$result_analysis$num_guild_a]
if (sum(species_a$kradius==Inf)>0)
species_a[species_a$kradius==Inf,]$kradius=100
species_a$kshell <- lnodes$kcorenum[1:mat$result_analysis$num_guild_a]
species_a$num <- seq(1:mat$result_analysis$num_guild_a)
species_b <- data.frame("num"=seq(1:mat$result_analysis$num_guild_b),"name"=rownames(mat$result_analysis$matrix))
species_b$kdegree <- lnodes$kdegree[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
species_b$kradius <- lnodes$kradius[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
if (sum(species_b$kradius==Inf)>0)
species_b[species_b$kradius==Inf,]$kradius=100
species_b$kshell <- lnodes$kcorenum[seq(mat$result_analysis$num_guild_a+1,mat$result_analysis$num_guild_a+mat$result_analysis$num_guild_b)]
species_b$num <- seq(1:mat$result_analysis$num_guild_b)
numberA <- mat$result_analysis$num_guild_a
numberB <- mat$result_analysis$num_guild_b
num_species <- numberA+numberB
M<-mat$result_analysis$matrix
binary_network = (sum(M>1)==0)
mat$binary_network <- binary_network
if(!is.null(progress))
mat$network_type <- ifelse(mat$binary_network,strings$value("LABEL_ZIGGURAT_INFO_BINARY"),strings$value("LABEL_ZIGGURAT_INFO_WEIGHTED"))
DegM <- M
DegM[DegM>1] <- 1
species_a$degree <- colSums(DegM)
species_b$degree <- rowSums(DegM)
# Vector that stores the node display order
if (orderby == "kradius"){
ordvectorA <- setkradiusorder(species_a)
ordvectorB <- rev(setkradiusorder(species_b))
}
if (orderby == "kdegree"){
ordvectorA <- setkdegreeorder(species_a)
ordvectorB <- rev(setkdegreeorder(species_b))
}
if (orderby == "degree"){
ordvectorA <- setdegreeorder(species_a)
ordvectorB <- rev(setdegreeorder(species_b))
}
species_a <- species_a[ordvectorA,]
species_b <- species_b[ordvectorB,]
if (!links_weight)
M[M>1]=1
M<-M[ordvectorB,ordvectorA]
num_b = species_b$num
num_a = species_a$num
longData<-melt(M)
mplots<- ggplot(longData, aes(x = Var2, y = Var1,fill=as.factor(value)))+geom_tile(alpha=1) + scale_fill_manual(values=c("white","red"))
longData$numA <- 0
longData$numB <- 0
names(longData) = c("speciesB","speciesA", "value","numB","numA")
mplots2<- ggplot(longData, aes(x = speciesA, y = speciesB,fill=as.factor(value)))+geom_tile(alpha=1) + scale_fill_manual(values=c("white","blue"))
for (i in 1:length(colnames(M)))
longData[longData$speciesA==colnames(M)[i],]$numA = create_labels(M,num_a,i,species_a,show_species=show_species_names,flip_matrix=flip_matrix,guild="A")
for (i in 1:length(rownames(M)))
longData[longData$speciesB==rownames(M)[i],]$numB = create_labels(M,num_b,i,species_b,show_species=show_species_names,flip_matrix=flip_matrix,guild="B")
lsize <- label_size
if (!show_species_names)
lsize <- lsize*1.2
lsizeantes <- lsize
maxnum <- max(numberA,numberB)
minnum <- min(numberA,numberB)
if ((maxnum+minnum)<40)
lsize <-lsize/2
else {
lsize <- lsize * (1-(0.0025 *(150-min(140,maxnum)))) * (maxnum+minnum)/(2*maxnum)
lsize <- lsize * (1-(nchar(max(species_a$name,species_b$name))/50)^3)
lsize <- min(lsize,ifelse((maxnum+minnum)>100,0.66,1)*lsizeantes/2)
}
if (numberA < numberB){
myflip_matrix <- !flip_matrix
mat$landscape <- !flip_matrix
} else {
mat$landscape <- !flip_matrix
myflip_matrix <- flip_matrix
}
p <- plot_m(longData,flip_matrix=myflip_matrix,nname=mat$network_name,
strA=mat$name_guild_a,strB=mat$name_guild_b,
links_weight = (links_weight && !binary_network),
colorA=color_guild_a,colorB=color_guild_b,lsize=lsize,
ncolor=color_links,show_title = show_title,
show_legend=show_legend)
plsize = plot_size
dppi = ppi
if (show_species_names)
aspect = (nrow(species_a)+10)/(nrow(species_b)+10)
else
aspect = (nrow(species_a)+1)/(nrow(species_b)+1)
imw <- plsize*dppi
imh <- plsize*dppi/aspect
if (mat$landscape){
plot_width <- max(imw,imh)
plot_height <- min(imw,imh)
} else {
plot_width <- min(imw,imh)
plot_height <- max(imw,imh)
}
if (print_to_file){
dir.create(mat$mat_argg$plotsdir, showWarnings = FALSE)
nfile <- paste0(plotsdir,mat$network_name,"_MATRIX_orderby_",orderby,".png")
png(nfile,width=plot_width,height=plot_height,res=dppi)
print(p)
dev.off()
}
if (!is.null(progress)){
ppi = 300
dir.create("www", showWarnings = FALSE)
dir.create("www/reports/", showWarnings = FALSE)
nfile <- paste0("www/reports/",mat$network_name,"_MATRIX.png")
if (mat$landscape){
plot_width <- max(imw,imh)
plot_height <- min(imw,imh)
}
else{
plot_width <- min(imw,imh)
plot_height <- max(imw,imh)
}
png(nfile,width=plot_width,height=plot_height,res=dppi)
print(p)
dev.off()
mat$matrix_file <- nfile
}
mat$aspect <- aspect
mat$plot <- p
mat$flip_results <- flip_matrix
mat$plot_width <- plot_width * dppi #= plsize
mat$plot_height <- plot_height * dppi #plsize/aspect
return(mat)
}
debugging = FALSE
if (debugging)
p <- matrix_graph("../data/","dattilo2014.csv",
print_to_file = TRUE, plotsdir ="plot_results/",
orderby = "kradius",ppi=300,
flip_matrix = FALSE, links_weight = FALSE,
show_species_names = TRUE,
show_title = TRUE,
show_legend = TRUE)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.