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Networks_fam_and_phylum.R
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Networks_fam_and_phylum.R
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# Import libraries
library(NetCoMi)
library(dplyr)
library(paletteer)
# Set seed to make results reproducible
set.seed(123)
# Load networks
nets_spring <- readRDS("Results/Networks/nets_spring_ColombRainforest.rds")
nets_cclasso <- readRDS("Results/Networks/nets_cclasso_ColombRainforest.rds")
# Load taxonomy df
tax_bact_familyrenamed <- read.csv("Data/tax_bact_familyrenamed.csv")
phyla <- as.factor(tax_bact_familyrenamed[, "Phylum"])
names(phyla) <- tax_bact_familyrenamed[, "Family"]
table(phyla)
# Define phylum colors
phylcol <- paletteer_d("ggsci::default_igv", 18)
phylcol[11] <- paletteer_d("ggsci::category20b_d3", 18)[15]
phylcol[16] <- paletteer_d("ggsci::category20b_d3", 18)[3]
phylcol[6] <- paletteer_d("ggsci::default_jco")[1]
phylcol[7] <- paletteer_d("ggsci::default_jco")[3]
phylcol[13] <- paletteer_d("ggsci::default_aaas")[2]
phylcol[2] <- paletteer_d("dichromat::SteppedSequential_5")[21]
# Colors used in the legend should be equally transparent as in the plot
# phylcol_transp <- colToTransp(phylcol, 20)
###############################################################################
########################### Analyze networks ##################################
###############################################################################
props_spring_nets <- netAnalyze(nets_spring,
centrLCC = FALSE,
avDissIgnoreInf = TRUE,
sPathNorm = TRUE,
clustMethod = "cluster_fast_greedy",
hubPar = "betweenness", #change it to define hub def
hubQuant = 0.9,
lnormFit = TRUE)
props_cclasso_nets <- netAnalyze(nets_cclasso,
centrLCC = FALSE,
avDissIgnoreInf = TRUE,
sPathNorm = TRUE,
clustMethod = "cluster_fast_greedy",
hubPar = "betweenness", #change it to define hub def
hubQuant = 0.9,
lnormFit = TRUE)
###############################################################################
########################### Visual comparison #################################
###############################################################################
# SPRING
# Degree as node size and hub definition
svg("Results/Figures/Family_and_Phylum_nets/svg/spring_nets_family_phyl_deg.svg", width=20, height=10)
# png("Results/Figures/Family_and_Phylum_nets/png/spring_nets_family_deg.png", width=1500, height=750)
spring_nets_plot <- plot(props_spring_nets,
layout = "spring",
sameLayout = FALSE,
layoutGroup = "union",
repulsion = 0.8,
nodeColor = "feature",
featVecCol = phyla,
colorVec = phylcol,
edgeTranspLow = 0,
edgeTranspHigh = 40,
nodeSize = "degree",
posCol = "#ac1214",
negCol = "#0d1fad",
shortenLabels = "intelligent",
labelLength = 7,
labelScale = FALSE,
rmSingles = TRUE,
cexNodes = 1.8,
cexLabels = 0.9,
nodeSizeSpread = 2.5,
cexHubLabels = 1,
hubBorderCol = "snow4",
cexTitle = 2.5,
groupNames = c("", ""))
legend(-0.10, 1, cex = 1, pt.cex = 1.5, title = 'Phylum:', title.adj = 0,
legend=levels(phyla), col = phylcol, bty = "n", pch = 16,
y.intersp = 0.7)
legend(-0.20, -0.72, title = "Estimated associations:", legend = c("+","-"),
col = c("#ac1214","#0d1fad"), inset = 0.02, cex = 1.5, lty = 1, lwd = 3,
bty = "n", horiz = TRUE, y.intersp = 0.5)
# Close device
dev.off()
# Betweenness as node size and hub definition
svg("Results/Figures/Family_and_Phylum_nets/svg/spring_nets_family_phyl_betw.svg", width=20, height=10)
# png("Results/Figures/Family_and_Phylum_nets/png/spring_nets_family_phyl_betw.png", width=1500, height=750)
spring_nets_plot <- plot(props_spring_nets,
layout = "spring",
sameLayout = FALSE,
layoutGroup = "union",
repulsion = 0.8,
nodeColor = "feature",
featVecCol = phyla,
colorVec = phylcol,
edgeTranspLow = 0,
edgeTranspHigh = 40,
nodeSize = "betweenness",
posCol = "#ac1214",
negCol = "#0d1fad",
shortenLabels = "intelligent",
labelLength = 7,
labelScale = FALSE,
rmSingles = TRUE,
cexNodes = 1.5,
cexLabels = 0.9,
nodeSizeSpread = 3,
cexHubLabels = 1,
hubBorderCol = "snow4",
cexTitle = 2.5,
groupNames = c("", ""))
legend(-0.10, 1, cex = 1, pt.cex = 1.5, title = 'Phylum:', title.adj = 0,
legend=levels(phyla), col = phylcol, bty = "n", pch = 16,
y.intersp = 0.7)
legend(-0.20, -0.72, title = "Estimated associations:", legend = c("+","-"),
col = c("#ac1214","#0d1fad"), inset = 0.02, cex = 1.5, lty = 1, lwd = 3,
bty = "n", horiz = TRUE, y.intersp = 0.5)
# Close device
dev.off()
# CCLASSO - Both nets
# Degree as node size and hub definition
svg("Results/Figures/Family_and_Phylum_nets/svg/cclasso_nets_family_phyl_deg.svg", width=20, height=10)
# png("Results/Figures/Family_and_Phylum_nets/png/cclasso_nets_family_phyl_deg.png", width=1500, height=750)
cclasso_nets_plot <- plot(props_cclasso_nets,
layout = "spring",
sameLayout = FALSE,
layoutGroup = "union",
repulsion = 0.9,
nodeColor = "feature",
featVecCol = phyla,
colorVec = phylcol,
edgeTranspLow = 0,
edgeTranspHigh = 40,
nodeSize = "degree",
posCol = "#ac1214",
negCol = "#0d1fad",
shortenLabels = "intelligent",
labelLength = 7,
labelScale = FALSE,
rmSingles = TRUE,
cexNodes = 2,
cexLabels = 0.9,
nodeSizeSpread = 3,
cexHubLabels = 1,
hubBorderCol = "snow4",
cexTitle = 2.5,
groupNames = c("", ""))
legend(-0.10, 1, cex = 1, pt.cex = 1.5, title = 'Phylum:', title.adj = 0,
legend=levels(phyla), col = phylcol, bty = "n", pch = 16,
y.intersp = 0.7)
legend(-0.20, -0.72, title = "Estimated associations:", legend = c("+","-"),
col = c("#ac1214","#0d1fad"), inset = 0.02, cex = 1.5, lty = 1, lwd = 3,
bty = "n", horiz = TRUE, y.intersp = 0.5)
# Close device
dev.off()
# Betweenness as node size and hub definition
# svg("Results/Figures/Family_and_Phylum_nets/svg/cclasso_nets_family_phyl_betw.svg", width=20, height=10)
png("Results/Figures/Family_and_Phylum_nets/png/cclasso_nets_family_phyl_betw.png", width=1500, height=750)
cclasso_nets_plot <- plot(props_cclasso_nets,
layout = "spring",
sameLayout = FALSE,
layoutGroup = "union",
repulsion = 0.9,
nodeColor = "feature",
featVecCol = phyla,
colorVec = phylcol,
edgeTranspLow = 0,
edgeTranspHigh = 40,
nodeSize = "betweenness",
posCol = "#ac1214",
negCol = "#0d1fad",
shortenLabels = "intelligent",
labelLength = 7,
labelScale = FALSE,
rmSingles = TRUE,
cexNodes = 2,
cexLabels = 0.9,
nodeSizeSpread = 4,
cexHubLabels = 1,
hubBorderCol = "snow4",
cexTitle = 2.5,
groupNames = c("Forest", "Pasture"))
legend(-0.10, 1, cex = 1, pt.cex = 1.5, title = 'Phylum:', title.adj = 0,
legend=levels(phyla), col = phylcol, bty = "n", pch = 16,
y.intersp = 0.7)
legend(-0.20, -0.72, title = "Estimated associations:", legend = c("+","-"),
col = c("#ac1214","#0d1fad"), inset = 0.02, cex = 1.5, lty = 1, lwd = 3,
bty = "n", horiz = TRUE, y.intersp = 0.5)
# Close device
dev.off()