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00_merge_area-size.Rmd
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00_merge_area-size.Rmd
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---
title: "R Notebook"
output: html_notebook
---
```{r}
wd <- dirname(getwd())
#Set working directory and folder structure
data_folder <- file.path(wd,'clinical_data')
#set plot folder for results
plot_folder <- file.path(wd,"results","merged")
set.seed(101100)
```
```{r}
wd <-dirname(getwd())
t86a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_86A.csv")))
t86b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_86B.csv")))
t86c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_86C.csv")))
t87a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_87A.csv")))
t87b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_87B.csv")))
t87c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_87C.csv")))
t88a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_88A.csv")))
t88b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_88B.csv")))
t88c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_88C.csv")))
t175a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_175A.csv")))
t175b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_175B.csv")))
t175c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_175C.csv")))
t176a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_176A.csv")))
t176b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_176B.csv")))
t176c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_176C.csv")))
t178a <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_178A.csv")))
t178b <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_178B.csv")))
t178c <- read.csv(file=file.path(wd,"clinical_data", paste("Resized_AreaMeasurements_Image_178C.csv")))
t86a$TMA <- "86A"
t86b$TMA <- "86B"
t86c$TMA <- "86C"
t87a$TMA <- "87A"
t87b$TMA <- "87B"
t87c$TMA <- "87C"
t88a$TMA <- "88A"
t88b$TMA <- "88B"
t88c$TMA <- "88C"
t175a$TMA <- "175A"
t175b$TMA <- "175B"
t175c$TMA <- "175C"
t176a$TMA <- "176A"
t176b$TMA <- "176B"
t176c$TMA <- "176C"
t178a$TMA <- "178A"
t178b$TMA <- "178B"
t178c$TMA <- "178C"
t.area <-rbind(t86a,t86b,t86c,t87a,t87b,t87c,t88a,t88b,t88c,t175a,t175b,t175c,t176a,t176b,t176c,t178a,t178b,t178c)
t.area$ImageID <- t.area$Metadata_acid
t.area <- t.area %>% select(c(AreaOccupied_AreaOccupied_StromaBinary,AreaOccupied_AreaOccupied_TumourBinary,AreaOccupied_AreaOccupied_TumourStromaBinary,TMA, ImageID)) #ImageNumber
t.area <-t.area %>% unite("TMA_ImageID", c(TMA, ImageID), remove=T)
colnames(t.area) <- c("Area_px_Stroma","Area_px_Tumour","Area_px_Core", "TMA_ImageID")
range(t.area$Area_px_Core)/1000000
hist(t.area$Area_px_Core/1000000)
summary(t.area$Area_px_Core/1000000)
t.area.mm <-
t.area %>%
dplyr::mutate_at(vars(Area_px_Stroma:Area_px_Core),
.funs = funs(. /1000000))
t.area.mm[t.area.mm$Area_px_Core>1,]
t.area.mm$ImageID <-NULL
colnames(t.area.mm) <- c("Area_mm_Stroma","Area_mm_Tumour","Area_mm_Core", "TMA_ImageID")
area <-left_join(t.area, t.area.mm, by="TMA_ImageID")
write.csv(area, file=file.path(data_folder, "area.csv"))
```
```{r}
colData(roi.sce) <-as.data.frame(colData(roi.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(pat.sce) <-as.data.frame(colData(pat.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(roi.sce) <-as.data.frame(colData(roi.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(roi.pat.sce) <-as.data.frame(colData(roi.pat.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(immune.u1) <-as.data.frame(colData(immune.u1)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(tumour.final) <-as.data.frame(colData(tumour.final)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(vessel.sce) <-as.data.frame(colData(vessel.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(vessel.vessel_pat.sce) <-as.data.frame(colData(vessel.vessel_pat.sce)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
colData(tumour.final) <-as.data.frame(colData(tumour.final)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
#immune
immune.o <-immune.final
immune.final <-immune.o
colData(immune.final) <-as.data.frame(colData(immune.final)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
dat.sce <- as_tibble(colData(immune.final))
dat.sce<-dat.sce %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE)
dat.sce <-DataFrame(dat.sce)
dat.sce<-merge(dat.sce, area, by="TMA_ImageID")
rownames(dat.sce) <-paste(dat.sce$TmaID, dat.sce$TmaBlock, dat.sce$ImageID, dat.sce$CellNumber, sep='_')
colData(immune.final) <- dat.sce
colnames(immune.final) <-rownames(dat.sce)
colData(immune.final)
colnames(colData(immune.final))
#tcells
tcells.o <-tcells.final
tcells.final <-tcells.o
colData(tcells.final) <-as.data.frame(colData(tcells.final)) %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE) %>% left_join(area, by="TMA_ImageID") %>% DataFrame()
dat.sce <- as_tibble(colData(tcells.final))
dat.sce$Area_mm_Core <-NULL
dat.sce$Area_mm_Stroma <-NULL
dat.sce$Area_mm_Tumour <-NULL
dat.sce$Area_px_Core <-NULL
dat.sce$Area_px_Stroma <-NULL
dat.sce$Area_px_Tumour <-NULL
dat.sce$TMA_Image <-NULL
dat.sce<-dat.sce %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE)
dat.sce <-DataFrame(dat.sce)
dat.sce<-merge(dat.sce, area, by="TMA_ImageID")
rownames(dat.sce) <-paste(dat.sce$TmaID, dat.sce$TmaBlock, dat.sce$ImageID, dat.sce$CellNumber, sep='_')
colData(tcells.final) <- dat.sce
colnames(tcells.final) <-rownames(dat.sce)
colData(tcells.final)
colnames(colData(tcells.final))
#tumour
dat.sce <- as_tibble(colData(tumour))
dat.sce<-dat.sce %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE)
dat.sce <-DataFrame(dat.sce)
dat.sce<-merge(dat.sce, area, by="TMA_ImageID")
rownames(dat.sce) <-paste(dat.sce$TmaID, dat.sce$TmaBlock, dat.sce$ImageID, dat.sce$CellNumber, sep='_')
colData(tumour) <- dat.sce
colnames(tumour) <-rownames(dat.sce)
colData(tumour)
colnames(colData(tumour))
#fibro
dat.sce <- as_tibble(colData(fibro.final.new))
dat.sce<-dat.sce %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE)
dat.sce <-DataFrame(dat.sce)
dat.sce<-merge(dat.sce, area, by="TMA_ImageID")
rownames(dat.sce) <-paste(dat.sce$TmaID, dat.sce$TmaBlock, dat.sce$ImageID, dat.sce$CellNumber, sep='_')
colData(fibro.final.new) <- dat.sce
colnames(fibro.final.new) <-rownames(dat.sce)
colData(fibro.final.new)
colnames(colData(fibro.final.new))
#vessel
dat.sce <- as_tibble(colData(vessel))
dat.sce<-dat.sce %>%
unite(TMA_ImageID, c(TMA, ImageID), sep = "_", remove = FALSE)
dat.sce <-DataFrame(dat.sce)
dat.sce<-merge(dat.sce, area, by="TMA_ImageID")
rownames(dat.sce) <-paste(dat.sce$TmaID, dat.sce$TmaBlock, dat.sce$ImageID, dat.sce$CellNumber, sep='_')
colData(vessel) <- dat.sce
colnames(vessel) <-rownames(dat.sce)
colData(vessel)
colnames(colData(vessel))
length(unique(tumour[,tumour$TMA=="88_A"]$ImageID))
order(unique(tumour[,tumour$TMA=="88_A"]$ImageID))
fibro$Area_mm
```
```{r}
wd <- dirname(getwd())
#Set working directory and folder structure
data_folder <- file.path(wd,'TMA_all',"SCE")
set.seed(101100)
saveRDS(tumour,file=file.path(data_folder,paste("tumour_sce_merge_minus_ctrl_area.rds")))
saveRDS(immune,file=file.path(data_folder,paste("immune_sce_merge_minus_ctrl_area.rds")))
saveRDS(tcells,file=file.path(data_folder,paste("tcells_sce_merge_minus_ctrl_area.rds")))
saveRDS(fibro,file=file.path(data_folder,paste("fibro_sce_merge_minus_ctrl_area.rds")))
saveRDS(vessel,file=file.path(data_folder,paste("vessel_sce_merge_minus_ctrl_area.rds")))
```