inst/scripts/colonization_3.phylograms.r
In surh/wheelP: Designing synthetic bacterial communities for predictable plant phenotypes
# (C) Copyright 2017 Sur Herrera Paredes
#
# This file is part of wheelP.
#
# wheelP is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wheelP is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with wheelP. If not, see <http://www.gnu.org/licenses/>.
library(AMOR)
library(wheelP)
# setwd("~/rhizogenomics/experiments/2017/today11/")
data(wheelP.mapsplit)
Dat <- wheelP.mapsplit
rm(wheelP.mapsplit)
Dat <- remove_taxons(Dat, as.character(Dat$Tax$ID[ Dat$Tax$Type == "contaminant" ]))
Dat$Map$Usable <- colSums(Dat$Tab)
Dat <- subset(Dat, Usable > 400)
Dat <- clean(Dat)
Dat <- subset(Dat, !(Experiment %in% c("Validation1","Validation2")),
drop = TRUE, clean = TRUE)
Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum, Group = NULL)
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP100.root <- p1$data
save(figS6B.plusP100.root, file = "figuredata/figS6B.plusP100.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP100.agar <- p1$data
save(figS6B.plusP100.agar, file = "figuredata/figS6B.plusP100.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP30.root <- p1$data
save(figS6B.plusP30.root, file = "figuredata/figS6B.plusP30.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP30.agar <- p1$data
save(figS6B.plusP30.agar, file = "figuredata/figS6B.plusP30.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP100.root <- p1$data
save(figS6B.minusP100.root, file = "figuredata/figS6B.minusP100.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP100.agar <- p1$data
save(figS6B.minusP100.agar, file = "figuredata/figS6B.minusP100.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP30.root <- p1$data
save(figS6B.minusP30.root, file = "figuredata/figS6B.minusP30.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP30.agar <- p1$data
save(figS6B.minusP30.agar, file = "figuredata/figS6B.minusP30.agar.rda")
rm(Dat.ord, p1, temp)
## Theoretical
data(Tax.colonization)
Tax <- subset(Tax.colonization, Type != "contaminant")
syncoms <- levels(Dat$Map$Bacteria)
Tab <- matrix(0, nrow = nrow(Tax), ncol = length(syncoms))
row.names(Tab) <- row.names(Tax)
colnames(Tab) <- syncoms
for(syncom in syncoms){
# syncom <- syncoms[1]
b1 <- substr(syncom,1,2)
b2 <- substr(syncom,3,4)
Tab[ row.names(subset(Tax,Block %in% c(b1,b2))), syncom ] <- 1
}
Theo <- create_dataset(Tab = Tab,
Map = data.frame(ID = syncoms,
Bacteria = factor(syncoms,
levels = levels(Dat$Map$Bacteria)),
row.names = syncoms),
Tax = Tax)
Theo.ord <- collapse_by_taxonomy(Theo,level = 5, sepchar = ";",FUN = sum, Group = NULL)
p1 <- phylogram(Theo.ord,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("theoretical.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.theoretical <- p1$data
save(figS6B.theoretical, file = "figuredata/figS6B.theoretical.rda")
rm(Tab,Tax,Tax.colonization,b1,b2,p1,syncom,syncoms,Theo,Theo.ord)
### Blocks
Blocks <- create_dataset(Tab = collapse_matrix(Dat$Tab,
groups = Dat$Tax$Block,
FUN = sum,
dim = 1),
Map = Dat$Map[,c("ID","Bacteria","Pre.Pi","Pos.Pi","Fraction")])
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP100.root <- p1$data
save(figS6C.plusP100.root, file = "figuredata/figS6C.plusP100.root.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP100.agar <- p1$data
save(figS6C.plusP100.agar, file = "figuredata/figS6C.plusP100.agar.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP30.root <- p1$data
save(figS6C.plusP30.root, file = "figuredata/figS6C.plusP30.root.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP30.agar <- p1$data
save(figS6C.plusP30.agar, file = "figuredata/figS6C.plusP30.agar.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP100.root <- p1$data
save(figS6C.minusP100.root, file = "figuredata/figS6C.minusP100.root.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP100.agar <- p1$data
save(figS6C.minusP100.agar, file = "figuredata/figS6C.minusP100.agar.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP30.root <- p1$data
save(figS6C.minusP30.root, file = "figuredata/figS6C.minusP30.root.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP30.agar <- p1$data
save(figS6C.minusP30.agar, file = "figuredata/figS6C.minusP30.agar.rda")
rm(p1,Blocks,temp)
surh/wheelP documentation built on May 7, 2019, 10:11 a.m.
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# (C) Copyright 2017 Sur Herrera Paredes
#
# This file is part of wheelP.
#
# wheelP is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wheelP is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with wheelP. If not, see <http://www.gnu.org/licenses/>.
library(AMOR)
library(wheelP)
# setwd("~/rhizogenomics/experiments/2017/today11/")
data(wheelP.mapsplit)
Dat <- wheelP.mapsplit
rm(wheelP.mapsplit)
Dat <- remove_taxons(Dat, as.character(Dat$Tax$ID[ Dat$Tax$Type == "contaminant" ]))
Dat$Map$Usable <- colSums(Dat$Tab)
Dat <- subset(Dat, Usable > 400)
Dat <- clean(Dat)
Dat <- subset(Dat, !(Experiment %in% c("Validation1","Validation2")),
drop = TRUE, clean = TRUE)
Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum, Group = NULL)
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP100.root <- p1$data
save(figS6B.plusP100.root, file = "figuredata/figS6B.plusP100.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP100.agar <- p1$data
save(figS6B.plusP100.agar, file = "figuredata/figS6B.plusP100.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP30.root <- p1$data
save(figS6B.plusP30.root, file = "figuredata/figS6B.plusP30.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.plusP30.agar <- p1$data
save(figS6B.plusP30.agar, file = "figuredata/figS6B.plusP30.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP100.root <- p1$data
save(figS6B.minusP100.root, file = "figuredata/figS6B.minusP100.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP100.agar <- p1$data
save(figS6B.minusP100.agar, file = "figuredata/figS6B.minusP100.agar.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP30.root <- p1$data
save(figS6B.minusP30.root, file = "figuredata/figS6B.minusP30.root.rda")
temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.minusP30.agar <- p1$data
save(figS6B.minusP30.agar, file = "figuredata/figS6B.minusP30.agar.rda")
rm(Dat.ord, p1, temp)
## Theoretical
data(Tax.colonization)
Tax <- subset(Tax.colonization, Type != "contaminant")
syncoms <- levels(Dat$Map$Bacteria)
Tab <- matrix(0, nrow = nrow(Tax), ncol = length(syncoms))
row.names(Tab) <- row.names(Tax)
colnames(Tab) <- syncoms
for(syncom in syncoms){
# syncom <- syncoms[1]
b1 <- substr(syncom,1,2)
b2 <- substr(syncom,3,4)
Tab[ row.names(subset(Tax,Block %in% c(b1,b2))), syncom ] <- 1
}
Theo <- create_dataset(Tab = Tab,
Map = data.frame(ID = syncoms,
Bacteria = factor(syncoms,
levels = levels(Dat$Map$Bacteria)),
row.names = syncoms),
Tax = Tax)
Theo.ord <- collapse_by_taxonomy(Theo,level = 5, sepchar = ";",FUN = sum, Group = NULL)
p1 <- phylogram(Theo.ord,facet = ~ Bacteria,nrow.legend = 8) +
scale_fill_brewer(palette = "Paired") +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("theoretical.phylogram.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6B.theoretical <- p1$data
save(figS6B.theoretical, file = "figuredata/figS6B.theoretical.rda")
rm(Tab,Tax,Tax.colonization,b1,b2,p1,syncom,syncoms,Theo,Theo.ord)
### Blocks
Blocks <- create_dataset(Tab = collapse_matrix(Dat$Tab,
groups = Dat$Tax$Block,
FUN = sum,
dim = 1),
Map = Dat$Map[,c("ID","Bacteria","Pre.Pi","Pos.Pi","Fraction")])
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP100.root <- p1$data
save(figS6C.plusP100.root, file = "figuredata/figS6C.plusP100.root.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP100.agar <- p1$data
save(figS6C.plusP100.agar, file = "figuredata/figS6C.plusP100.agar.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP30.root <- p1$data
save(figS6C.plusP30.root, file = "figuredata/figS6C.plusP30.root.rda")
temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("plusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.plusP30.agar <- p1$data
save(figS6C.plusP30.agar, file = "figuredata/figS6C.plusP30.agar.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP100.root <- p1$data
save(figS6C.minusP100.root, file = "figuredata/figS6C.minusP100.root.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "100 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "+Pi,0.5%Suc => 100 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP100.agar <- p1$data
save(figS6C.minusP100.agar, file = "figuredata/figS6C.minusP100.agar.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Root")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP30.root <- p1$data
save(figS6C.minusP30.root, file = "figuredata/figS6C.minusP30.root.rda")
temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
Pos.Pi == "30 uM,0%Suc" &
Fraction == "Agar")
p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
scale_fill_manual(values = rev(RColorBrewer::brewer.pal(n = 9,name = "PiYG"))) +
ggtitle(label = "-Pi,0.5%Suc => 30 uM,0%Suc") +
theme(axis.text.x = element_blank(),
strip.text = element_text(face = "bold", size = 12),
axis.title = element_text(face = "bold", size = 16),
axis.text.y = element_text(size = 14, color = "black", angle = 0),
panel.background = element_blank(),
axis.ticks.x = element_blank(),
strip.background = element_blank())
p1
ggsave("minusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
dir.create("figuredata/")
figS6C.minusP30.agar <- p1$data
save(figS6C.minusP30.agar, file = "figuredata/figS6C.minusP30.agar.rda")
rm(p1,Blocks,temp)
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