.Rhistory

library(tidyverse)
library(treemapify)
#secCellFie
taskInfo.sec <- openxlsx::read.xlsx("Generate_essentialRxns_manual/essentialRxn_notebook2022.xlsx", sheet="TaskInfo")
count.system.sec <- table(taskInfo.sec$System) %>% data.table() %>% setNames(c("System", "count")) %>%
mutate(System=toupper(System)) %>%
mutate(Pathway="Secretory Pathway")
#secCellFie
taskInfo.sec <- openxlsx::read.xlsx("Generate_essentialRxns_manual/essentialRxn_notebook2022.xlsx", sheet="TaskInfo")
count.system.sec <- table(taskInfo.sec$System) %>% data.table() %>% setNames(c("System", "count")) %>%
mutate(System=toupper(System)) %>%
mutate(Pathway="Secretory Pathway")
#metCellFie
# fread("CellFie/genepattern/outtmp/taskInfo.csv")
taskInfo.met <- fread("taskInfo_edit.csv") %>% setNames(colnames(taskInfo.sec))
count.system.met <- table(taskInfo.met$System) %>% data.table() %>% setNames(c("System", "count")) %>%
mutate(Pathway="Metabolic Pathway")
ggplot(count.system.sec, aes(x="", y=count, fill=System)) +
geom_bar(stat="identity", width=1) +
#geom_text(aes(y=ypos, label= percent, size=4)) +
coord_polar("y", start=0) +
theme_void() +
scale_fill_brewer(palette="Set2")
cellfie.tree <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
count.system <- rbind(count.system.met, count.system.sec)
count.system <- rbind(count.system.met, count.system.sec)
cellfie.tree <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
count.system <- rbind(count.system.met, count.system.sec)
cellfie.tree <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
count.system <- rbind(count.system.met, count.system.sec)
cellfie.tree2 <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
count.system <- rbind(count.system.met, count.system.sec)
cellfie.tree2 <- ggplot(count.system, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
#geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
View(count.system)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
mutate(Pathway="Metabolic Pathway")
View(count.system.met2)
names(count.system.met)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(count.system.met, c("System", "Pathway")))
View(taskInfo.met)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")))
dim(count.system.met2)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique())
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
dim(count.system.met2)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
#geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
#geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
#geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
#geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
#geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray47", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
cellfie.tree2
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
png("Figures/CellFie_tree_v2.png", width=500, height=500)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
dev.off()
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
png("Figures/CellFie_tree_v2.png", width=500, height=500)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
dev.off()
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree.svg", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.svg", cellfie.tree2, width = 9, height = 6)
count.system <- rbind(count.system.met, count.system.sec)
cellfie.tree <- ggplot(count.system, aes(area=count, subgroup=Pathway, subgroup2= System, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("plum1", "palegreen"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
#geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree.svg", cellfie.tree, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=F) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=3, reflow=F) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=T, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="centre", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray99", min.size=0, reflow=T) +
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.7, colour="gray27", min.size=0, reflow=T) +
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray27", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.7, colour="black", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="black", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.7, colour="gray99", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="black", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.6, colour="gray99", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="black", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.6, colour="gray99", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray99", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.6, colour="gray60", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray99", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.8, colour="gray48", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray99", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.8, colour="gray54", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)
count.system.met2 <- table(taskInfo.met$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.met, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Metabolic Pathway")
count.system.sec2 <- table(taskInfo.sec$Subsystem) %>% data.table() %>% setNames(c("Subsystem", "count")) %>%
left_join(select(taskInfo.sec, c("System", "Subsystem")) %>% unique()) %>%
mutate(Pathway="Secretory Pathway")
count.system2 <- rbind(count.system.met2, count.system.sec2)
cellfie.tree2 <- ggplot(count.system2, aes(area=count, subgroup=System, subgroup2= Subsystem, fill=Pathway))+
labs(fill = "Cellfie Pathway")+
scale_fill_manual(values=c("#8B008B", "#008B45"))+
geom_treemap(colour="white")+
geom_treemap_subgroup2_border(colour="gray61", size=1) +
geom_treemap_subgroup_border(colour="gray61", size=4) +
geom_treemap_subgroup_text(place="centre", grow=F, alpha=1, colour="gray99", min.size=0, reflow=T) + #gray99
geom_treemap_subgroup2_text(place="top", grow=F, alpha=0.8, colour="gray27", min.size=0, reflow=T) + #gray27
theme(legend.title=element_text(size=15), legend.text = element_text(size=13))
ggsave("Figures/CellFie_tree_v2.png", cellfie.tree2, width = 9, height = 6)