library(readr)
library(ggtree)
library(treeio)
library(DESeq2)
library(ggplot2)
library(stringr)
library(tidyverse)
df_handle<-function(
otu_table,
treefile,
tiplabelfile,
pattern){
dat01<-read_tsv(otu_table)
tiplabgroup<-read_tsv(tiplabelfile)
tree<-read.tree(treefile)
new.tree<-full_join(tree,tiplabgroup,by='label')
ggtree(new.tree)+
#geom_tiplab(align = TRUE)+
geom_tippoint(aes(color=GROUP))+
#xlim(NA,1.5)+
theme(legend.position = "none")-> p1
group.info.01<-data.frame(
row.names = dat01 %>% select(matches(pattern)) %>%
colnames(),
conditions = c(rep("trt",5),
rep("ctl",5))
)
group.info.01$conditions<-factor(group.info.01$conditions)
dat01 %>%
select(matches(paste(pattern,"OTU ID",sep = "|"))) %>%
column_to_rownames('OTU ID') -> dat01.1
dds <- DESeq2::DESeqDataSetFromMatrix(countData = dat01.1,
colData=group.info.01,
design = ~ conditions)
dds_res <- DESeq2::DESeq(dds, sfType = "poscounts")
res <- results(dds_res,
tidy=T,
format="DataFrame",
contrast = c("conditions","trt","ctl"))
res %>%
mutate(str_extract(row,"f__\\S+;") %>%
str_split_fixed(pattern = ";",n=10) %>%
as.data.frame() %>%
select(1)) -> res.01
res.01[which(res.01$V1%in%tree$tip.label),] %>%
filter(!is.na(log2FoldChange)) %>%
group_by(V1) %>%
summarise(log2FoldChange=mean(log2FoldChange)) -> res.02
merge(res.02,tiplabgroup,by.x='V1',by.y="label") -> res.02
res.02$V1<-factor(res.02$V1,
levels = p1$data %>% na.omit() %>% arrange(y) %>% pull(label))
dat01.1 %>% rownames_to_column(var = "family") %>%
mutate(str_extract(family,"f__\\S+;") %>%
str_split_fixed(pattern = ";",n=10) %>%
as.data.frame() %>%
select(1)) -> dat01.2
dat01.1 %>% rownames_to_column(var = "family") %>%
mutate(str_extract(family,"f__\\S+;") %>%
str_split_fixed(pattern = ";",n=10) %>%
as.data.frame() %>%
select(1)) %>%
merge(tiplabgroup,by.x="V1",by.y='label') %>%
select(-c('family','GROUP')) %>%
group_by(V1) %>%
summarise_all(mean) %>%
mutate(mrd=rowSums(.[2:11])/10) %>%
select(V1,mrd) -> dat01.2
res.02$V1<-str_replace(res.02$V1,"f__","")
res.02$GROUP<-str_replace(res.02$GROUP,"c__","")
dat01.2$V1<-str_replace(dat01.2$V1,"f__","")
new.tree@phylo$tip.label<-
str_replace(new.tree@phylo$tip.label,
"f__","")
new.tree@data$GROUP<-
str_replace(new.tree@data$GROUP,
"c__","")
return(list(bubble.1 = res.02,
bubble.2 = dat01.2,
tree.1 = new.tree))
}
bubble_figure<-function(dat){
ggplot(data=dat,
aes(x=log2FoldChange,y=V1))+
geom_vline(xintercept = 0,lty="dashed",
color="grey",size=1)+
geom_point(aes(size=log2FoldChange,
fill=GROUP),
shape=21)+
guides(size='none',
fill=guide_legend(ncol=6))+
scale_fill_discrete(name=NULL)+
#ggtitle("F_0_20VSW_0_20")+
theme_minimal()+
theme(legend.position = "bottom",
legend.direction = "vertical",
legend.justification = c(0,0),
axis.ticks.y = element_blank(),
axis.text.y = element_blank(),
panel.grid = element_blank(),
axis.line.x = element_line(),
axis.ticks.x = element_line())+
labs(y=NULL) -> p
return(p)
}
#bubble_figure(plot_data[["bubble.1"]])
dat01<-read_tsv("data/20220414/data/otu_taxon_otu.full.xls")
dat01 %>% colnames()
dat01 %>% select(matches("[FW]\\d_0_20")) %>% colnames()
dat01 %>% select(matches("[FW]\\d_20_40")) %>% colnames()
dat01 %>% select(matches("[FW]\\d_40_60")) %>% colnames()
dat01 %>% select(matches("[HW]\\d_0_20")) %>% colnames()
dat01 %>% select(matches("[HW]\\d_20_40")) %>% colnames()
dat01 %>% select(matches("[HW]\\d_40_60")) %>% colnames()
dat01 %>% select(matches("[MW]\\d_0_20")) %>% colnames()
dat01 %>% select(matches("[MW]\\d_20_40")) %>% colnames()
dat01 %>% select(matches("[MW]\\d_40_60")) %>% colnames()
df_handle(otu_table = "data/20220414/data/otu_taxon_otu.full.xls",
treefile = "data/20220414/data/phylo_tree .tre",
tiplabelfile = "data/20220414/data/species_group .xls",
pattern = "[FW]\\d_0_20") -> plot_data
trt_ctl<-c("[FW]\\d_0_20","[FW]\\d_20_40","[FW]\\d_40_60",
"[HW]\\d_0_20","[HW]\\d_20_40","[HW]\\d_40_60",
"[MW]\\d_0_20","[MW]\\d_20_40","[MW]\\d_40_60")
plot_list = list()
for (i in 1:9){
df_handle(otu_table = "data/20220414/data/otu_taxon_otu.full.xls",
treefile = "data/20220414/data/phylo_tree .tre",
tiplabelfile = "data/20220414/data/species_group .xls",
pattern = trt_ctl[i]) -> plot_data
#print(plot_data)
#print(bubble_figure(plot_data[["bubble.1"]]))
bubble_figure(plot_data[["bubble.1"]]) -> plot_list[[i]]
}
p1<-ggtree(plot_data[["tree.1"]])+
geom_tiplab(align = T,offset = 0.01)+
geom_tippoint(aes(color=GROUP))+
xlim(NA,2)+
theme(legend.position = "none")
p1
p1+plot_spacer()+
(plot_list[[1]]+
plot_list[[2]]+
plot_list[[3]]+
plot_list[[4]]+
plot_list[[5]]+
plot_list[[6]]+
plot_list[[7]]+
plot_list[[8]]+
plot_list[[9]]+
plot_layout(guides = "collect",
nrow=1)&theme(legend.position = "bottom"))+
plot_layout(widths = c(1,1,9))
image.png