WSS28model/Dia plots/Dia2CircularPlots.R
In NOAA-EDAB/RpathQNM: What the Package Does (One Line, Title Case)
# Read in dia files and make circlize figures
# based on code in Geret DePiper's repo for summer flounder modeling
# https://github.com/NEFSC/READ-SSB-DePiper_Summer_Flounder_Conceptual_Models/blob/master/circulargraphrcode_Summer_Flounder_v2.R
#
# Citation:
# Geret DePiper, Sarah Gaichas, Brandon Muffley, Greg Ardini, Jeffrey Brust,
# Jessica Coakley, Kiley Dancy, G Warren Elliott, Dustin C Leaning, Douglas Lipton,
# Jason McNamee, Charles Perretti, Kirby Rootes-Murdy, Michael J Wilberg,
# Learning by doing: collaborative conceptual modelling as a path forward in
# ecosystem-based management, ICES Journal of Marine Science, Volume 78, Issue 4,
# August 2021, Pages 1217–1228, https://doi.org/10.1093/icesjms/fsab054
#
#
library(QPress)
library(chorddiag)
library(circlize)
library(RColorBrewer)
# in project won't look for files below top directory
#edges <- QPress::model.dia(here::here("WSS28model/Dia plots/SarahWSS1.dia"))
edges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS6.dia"))
## Examine unweighted adjacency matrix
fullmod <- adjacency.matrix(edges, labels=TRUE)
fullmodnoself <- adjacency.matrix(edges, labels=TRUE)
## remove self loops
diag(fullmodnoself) <- 0
feweredges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS1.dia"))
fewestedges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS5.dia"))
smallestmod <- adjacency.matrix(fewestedges, labels=TRUE)
smallestmodnoself <- adjacency.matrix(fewestedges, labels=TRUE)
## remove self loops
diag(smallestmodnoself) <- 0
# test plots
#circlize::chordDiagram(fullmod)
#circlize::chordDiagram(smallestmod)
# standardize group positions, widths, and colors across both models
phyto <- c("Phytoplankton")
zoo <- c("Gelatinous zoop", "Macrozoop", "Mesozoop", "Microflora", "Microzoop")
benthos <- c("Bivalves", "Megabenthos", "Meiofauna", "Other molluscs", "Shrimps",
"Small crab other arthropoda", "Worms")
fish <- c("D piscivores", "L benthivores", "Large pelagics", "Other pelagic mesopelagic",
"Sharks", "Skates", "Squids")
smallpel <- c("Small pelagics")
birdsmammals <- c("Sea birds", "Toothed cetaceans", "Whales")
seals <- c("Seals")
fishery <- c("Fishery")
detritus <- c("Detritus", "Discards")
mod_C <- brewer.pal(9,"Set1")
# Function for any of these models
# This is Geret's original pdf maker
pdfmod <- function(modadjmat, plotname){
mod_Colors <- data.frame(row.names(modadjmat))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(modadjmat,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
pdf(here::here(paste0(plotname,".pdf")),width = 6.69291, height=6.69291)
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[5],mod_C[6],mod_C[7],mod_C[8], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(plotname), line=-35))
dev.off()
}
#pdfmod(fullmod, "Fullmodel")
#pdfmod(smallestmod, "Smallmodel")
# this function plots individual models on their own scale, not great for comparisons
plotmod <- function(modadjmat, plotname){
mod_Colors <- data.frame(row.names(modadjmat))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(modadjmat,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
png(here::here(paste0(plotname,".png")))
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[1],mod_C[6],mod_C[1],mod_C[1], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(plotname), line=-35))
dev.off()
}
#plotmod(fullmod, "Full model")
#plotmod(fullmodnoself, "Full-model-no-diag")
#plotmod(smallestmod, "Smallest model")
# This function plots the full model but only colors links in the compared model.
plotdiff <- function(full, comp, compname){
mod_Colors <- data.frame(row.names(full))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(full,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
# define colors for mod2
mod2_Colors <- data.frame(row.names(comp))
colnames(mod2_Colors) <- "Focus"
mod2_Colors$Color[mod2_Colors$Focus%in%phyto] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%zoo] <- mod_C[2]
mod2_Colors$Color[mod2_Colors$Focus%in%benthos] <- mod_C[3]
mod2_Colors$Color[mod2_Colors$Focus%in%fish] <- mod_C[4]
mod2_Colors$Color[mod2_Colors$Focus%in%smallpel] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod2_Colors$Color[mod2_Colors$Focus%in%seals] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%fishery] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%detritus] <- mod_C[9]
compdf <- data.frame(from = rep(rownames(comp), times = ncol(comp)),
to = rep(colnames(comp), each = nrow(comp)),
value = as.vector(comp),
stringsAsFactors = FALSE) |>
dplyr::filter(value != 0) |>
dplyr::left_join(mod2_Colors, by=c("from" = "Focus")) |>
dplyr::select(-value)
#png(here::here(paste0(compname,".png")), width = 600, height = 600)
#jpeg(here::here(paste0(compname,".jpeg")), width = 600, height = 600)
#pdf(here::here(paste0(compname,".pdf")), width = 10, height = 10)
tiff(here::here(paste0(compname, ".tiff")),
width = 8, # Increase width to improve detail
height = 8, # Increase height to improve detail
units = "in",
res = 600) # Increase resolution to 600 DPI for high quality
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
col = compdf,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[1],mod_C[6],mod_C[1],mod_C[1], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(compname), line=-35))
dev.off()
}
plotdiff(fullmod, fullmodnoself, "Full-model-no-diag")
#plotdiff(fullmod, smallestmod, "Smallest-model")
plotdiff(fullmod, smallestmodnoself, "Smallest-model-no-diag")
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# Read in dia files and make circlize figures
# based on code in Geret DePiper's repo for summer flounder modeling
# https://github.com/NEFSC/READ-SSB-DePiper_Summer_Flounder_Conceptual_Models/blob/master/circulargraphrcode_Summer_Flounder_v2.R
#
# Citation:
# Geret DePiper, Sarah Gaichas, Brandon Muffley, Greg Ardini, Jeffrey Brust,
# Jessica Coakley, Kiley Dancy, G Warren Elliott, Dustin C Leaning, Douglas Lipton,
# Jason McNamee, Charles Perretti, Kirby Rootes-Murdy, Michael J Wilberg,
# Learning by doing: collaborative conceptual modelling as a path forward in
# ecosystem-based management, ICES Journal of Marine Science, Volume 78, Issue 4,
# August 2021, Pages 1217–1228, https://doi.org/10.1093/icesjms/fsab054
#
#
library(QPress)
library(chorddiag)
library(circlize)
library(RColorBrewer)
# in project won't look for files below top directory
#edges <- QPress::model.dia(here::here("WSS28model/Dia plots/SarahWSS1.dia"))
edges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS6.dia"))
## Examine unweighted adjacency matrix
fullmod <- adjacency.matrix(edges, labels=TRUE)
fullmodnoself <- adjacency.matrix(edges, labels=TRUE)
## remove self loops
diag(fullmodnoself) <- 0
feweredges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS1.dia"))
fewestedges <- QPress::model.dia(here::here("WSS28model/Dia plots/WSS5.dia"))
smallestmod <- adjacency.matrix(fewestedges, labels=TRUE)
smallestmodnoself <- adjacency.matrix(fewestedges, labels=TRUE)
## remove self loops
diag(smallestmodnoself) <- 0
# test plots
#circlize::chordDiagram(fullmod)
#circlize::chordDiagram(smallestmod)
# standardize group positions, widths, and colors across both models
phyto <- c("Phytoplankton")
zoo <- c("Gelatinous zoop", "Macrozoop", "Mesozoop", "Microflora", "Microzoop")
benthos <- c("Bivalves", "Megabenthos", "Meiofauna", "Other molluscs", "Shrimps",
"Small crab other arthropoda", "Worms")
fish <- c("D piscivores", "L benthivores", "Large pelagics", "Other pelagic mesopelagic",
"Sharks", "Skates", "Squids")
smallpel <- c("Small pelagics")
birdsmammals <- c("Sea birds", "Toothed cetaceans", "Whales")
seals <- c("Seals")
fishery <- c("Fishery")
detritus <- c("Detritus", "Discards")
mod_C <- brewer.pal(9,"Set1")
# Function for any of these models
# This is Geret's original pdf maker
pdfmod <- function(modadjmat, plotname){
mod_Colors <- data.frame(row.names(modadjmat))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(modadjmat,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
pdf(here::here(paste0(plotname,".pdf")),width = 6.69291, height=6.69291)
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[5],mod_C[6],mod_C[7],mod_C[8], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(plotname), line=-35))
dev.off()
}
#pdfmod(fullmod, "Fullmodel")
#pdfmod(smallestmod, "Smallmodel")
# this function plots individual models on their own scale, not great for comparisons
plotmod <- function(modadjmat, plotname){
mod_Colors <- data.frame(row.names(modadjmat))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(modadjmat,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
png(here::here(paste0(plotname,".png")))
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[1],mod_C[6],mod_C[1],mod_C[1], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(plotname), line=-35))
dev.off()
}
#plotmod(fullmod, "Full model")
#plotmod(fullmodnoself, "Full-model-no-diag")
#plotmod(smallestmod, "Smallest model")
# This function plots the full model but only colors links in the compared model.
plotdiff <- function(full, comp, compname){
mod_Colors <- data.frame(row.names(full))
colnames(mod_Colors) <- "Focus"
mod_Colors$Color[mod_Colors$Focus%in%phyto] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%zoo] <- mod_C[2]
mod_Colors$Color[mod_Colors$Focus%in%benthos] <- mod_C[3]
mod_Colors$Color[mod_Colors$Focus%in%fish] <- mod_C[4]
mod_Colors$Color[mod_Colors$Focus%in%smallpel] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod_Colors$Color[mod_Colors$Focus%in%seals] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%fishery] <- mod_C[1]
mod_Colors$Color[mod_Colors$Focus%in%detritus] <- mod_C[9]
mod_Groups <- mod_Colors
mod_Groups$Group[mod_Groups$Focus%in%phyto] <- "Phytoplankton"
mod_Groups$Rank[mod_Groups$Focus%in%phyto] <- 1
mod_Groups$Group[mod_Groups$Focus%in%zoo] <- "Zooplankton"
mod_Groups$Rank[mod_Groups$Focus%in%zoo] <- 2
mod_Groups$Group[mod_Groups$Focus%in%benthos] <- "Benthos"
mod_Groups$Rank[mod_Groups$Focus%in%benthos] <- 3
mod_Groups$Group[mod_Groups$Focus%in%fish] <- "Fish/Squid"
mod_Groups$Rank[mod_Groups$Focus%in%fish] <- 4
mod_Groups$Group[mod_Groups$Focus%in%smallpel] <- "Small pelgics"
mod_Groups$Rank[mod_Groups$Focus%in%smallpel] <- 5
mod_Groups$Group[mod_Groups$Focus%in%birdsmammals] <- "Birds/Mammals"
mod_Groups$Rank[mod_Groups$Focus%in%birdsmammals] <- 6
mod_Groups$Group[mod_Groups$Focus%in%seals] <- "Seals"
mod_Groups$Rank[mod_Groups$Focus%in%seals] <- 7
mod_Groups$Group[mod_Groups$Focus%in%fishery] <- "Fishery"
mod_Groups$Rank[mod_Groups$Focus%in%fishery] <- 8
mod_Groups$Group[mod_Groups$Focus%in%detritus] <- "Detritus"
mod_Groups$Rank[mod_Groups$Focus%in%detritus] <- 9
mod_edges <- cbind(full,mod_Colors)
mod_Colors <- mod_Colors[order(mod_Colors$Color,mod_Colors$Focus),]
mod_Colors <- matrix(mod_Colors$Color,dimnames=list(mod_Colors$Focus,"Color"))
mod_edges <- mod_edges[order( mod_edges$Color,mod_edges$Focus),]
mod_edges$Color <- NULL
mod_edges$Focus <- NULL
mod_edges <- data.matrix(mod_edges)
Border_mat <- matrix(1,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_mat) <- rownames(mod_edges)
colnames(Border_mat) <- colnames(mod_edges)
#Border_mat[Grand_Banks_edges < 0] = 2
Border_Col <- matrix("white",nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_Col) <- rownames(mod_edges)
colnames(Border_Col) <- colnames(mod_edges)
#Border_Col[Grand_Banks_edges < 0] = "black"
Border_w <- matrix(.0001,nrow=nrow(mod_edges),ncol=ncol(mod_edges))
rownames(Border_w) <- rownames(mod_edges)
colnames(Border_w) <- colnames(mod_edges)
# define colors for mod2
mod2_Colors <- data.frame(row.names(comp))
colnames(mod2_Colors) <- "Focus"
mod2_Colors$Color[mod2_Colors$Focus%in%phyto] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%zoo] <- mod_C[2]
mod2_Colors$Color[mod2_Colors$Focus%in%benthos] <- mod_C[3]
mod2_Colors$Color[mod2_Colors$Focus%in%fish] <- mod_C[4]
mod2_Colors$Color[mod2_Colors$Focus%in%smallpel] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%birdsmammals] <- mod_C[5]
mod2_Colors$Color[mod2_Colors$Focus%in%seals] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%fishery] <- mod_C[1]
mod2_Colors$Color[mod2_Colors$Focus%in%detritus] <- mod_C[9]
compdf <- data.frame(from = rep(rownames(comp), times = ncol(comp)),
to = rep(colnames(comp), each = nrow(comp)),
value = as.vector(comp),
stringsAsFactors = FALSE) |>
dplyr::filter(value != 0) |>
dplyr::left_join(mod2_Colors, by=c("from" = "Focus")) |>
dplyr::select(-value)
#png(here::here(paste0(compname,".png")), width = 600, height = 600)
#jpeg(here::here(paste0(compname,".jpeg")), width = 600, height = 600)
#pdf(here::here(paste0(compname,".pdf")), width = 10, height = 10)
tiff(here::here(paste0(compname, ".tiff")),
width = 8, # Increase width to improve detail
height = 8, # Increase height to improve detail
units = "in",
res = 600) # Increase resolution to 600 DPI for high quality
print(chordDiagram(mod_edges, directional=0,
grid.col = mod_Colors,
col = compdf,
row.col = mod_Colors,
link.lty = Border_mat,
link.lwd = Border_w,
link.border = Border_Col,
annotationTrack="grid",preAllocateTracks= list(track.height=0.5)))
print(circos.trackPlotRegion(track.index=1, panel.fun= function (x,y){
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim),ylim[1],sector.name,facing="clockwise", niceFacing=TRUE, adj =c(0,0.5), cex=.6)
}, bg.border=NA) )
# print(legend(x=-1.1,y = 1.09,legend = c("Phytoplankton","Zooplankton","Benthos","Fish/Squid","Small pelgics","Birds/Mammals","Seals","Fishery", "Detritus"),
# lty= c(1,1,1,1,1,1,1,1), lwd=c(5,5,5,5,5,5,5,5),
# col =c(mod_C[1],mod_C[2],mod_C[3],mod_C[4],mod_C[1],mod_C[6],mod_C[1],mod_C[1], mod_C[9]), ncol=1, cex = .75, bg = NULL, box.col=NULL, bty = "n"))
# print(title(main=paste(compname), line=-35))
dev.off()
}
plotdiff(fullmod, fullmodnoself, "Full-model-no-diag")
#plotdiff(fullmod, smallestmod, "Smallest-model")
plotdiff(fullmod, smallestmodnoself, "Smallest-model-no-diag")
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