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devtools::install_version("seurat",version="v2.3.4")
devtools::install_version("Seurat",version="2.3.4")
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal.RData",
"inst/Inj9dFACS/Inj9dFACS.RData",
"inst/InjCombined/InjCombined.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined.RData",
"inst/UninjMesenchymal/UninjMesenchymal.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
stringsAsFactors=F)
i <- 1
load(filemap$new[i])
temp_seur <- UpdateSeuratObject(eb1S)
temp_seur
temp_seur@dr$ica
temp_seur@dr$pca
temp_seur@dr$tsne
eb1S <- UpdateSeuratObject(eb1S)
rm(temp_seur)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal.RData",
"inst/Inj9dFACS/Inj9dFACS.RData",
"inst/InjCombined/InjCombined.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined.RData",
"inst/UninjMesenchymal/UninjMesenchymal.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
filemap$new[1]
filemap$v2[1]
for (i in 1:6) {
load(filemap$new[i])
eb1S <- UpdateSeuratObject(eb1S)
save(eb1S,file=filemap$v2[i])
}
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal.RData",
"inst/Inj9dFACS/Inj9dFACS.RData",
"inst/InjCombined/InjCombined.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined.RData",
"inst/UninjMesenchymal/UninjMesenchymal.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
for (i in 1:6) {
load(filemap$new[i])
eb1S <- UpdateSeuratObject(eb1S)
save(eb1S,file=filemap$v2[i])
}
devtools::update_packages()
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal.RData",
"inst/Inj9dFACS/Inj9dFACS.RData",
"inst/InjCombined/InjCombined.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined.RData",
"inst/UninjMesenchymal/UninjMesenchymal.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$old[i])
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- getMD(eb1S)[temp_cells,names(data_for_scClustViz$cl)]
temp_seur <- UpdateSeuratObject(eb1S)
load(filemap$v2[i])
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- getMD(eb1S)[temp_cells,names(data_for_scClustViz$cl)]
temp_seur <- UpdateSeuratObject(eb1S)
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
colnames(temp_seur)
temp_cell
temp_cells
SubsetData(temp_seur,cells=temp_cells)
subset(temp_seur,cells=temp_cells)
temp_seur <- subset(temp_seur,cells=temp_cells)
pDat
if (all(rownames(pDat) == rownames(getMD(eb1S)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_cl
rownames(temp_cl) == colnames(temp_seur)
rownames(temp_cl)
rownames(getMD(temp_seur))
dim(pDat)
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- getMD(eb1S)[temp_cells,names(data_for_scClustViz$cl)]
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_seur <- subset(temp_seur,cells=temp_cells)
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
head(pDat)
[email protected] <- pDat[temp_cells,]
assign(paste(temp_name,"seur",sep="_"),temp_seur)
temp_name
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- getMD(eb1S)[temp_cells,names(data_for_scClustViz$cl)]
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_seur <- subset(temp_seur,cells=temp_cells)
[email protected] <- pDat[temp_cells,]
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl)
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
data_for_scClustViz$cl
dim(data_for_scClustViz$cl)
data_for_scClustViz$cl[names(temp_cells),]
temp_cl <- data_for_scClustViz$cl[names(temp_cells),]
rownames(temp_cl) <- temp_cells
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_"),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
paste(temp_name,"seur",sep="_")
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
for (i in 1:5) {
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_cl <- getMD(temp_seur)[,names(data_for_scClustViz$cl)]
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
}
load("~/MK_MSN/MouseSciaticNerve/inst/Inj9dBeads/Inj9dBeads.RData")
getEmb(Inj9dBeads_seur)
getEmb(Inj9dBeads_seur,"ica")
i <- 1
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
i <- 1
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_cl <- getMD(temp_seur)[,names(data_for_scClustViz$cl)]
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA",storeAllDE=F)
i
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
head(DEvsRest(temp_scv$res.3))
head(DEvsRest(temp_scv$res.3)[[1]])
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
filemap$old[i]
sub(".RData","_savedRes.RData",filemap$old[i])
sub("_old.RData","_savedRes.RData",filemap$old[i])
sub("old.RData","savedRes.RData",filemap$old[i])
load(sub("old.RData","savedRes.RData",filemap$old[i]))
head(data_for_scClustViz$cl)
temp_cl <- data_for_scClustViz$cl[names(temp_cells),savedRes,drop=F]
str(temp_cl)
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
# for (i in 1:6) {
# load(filemap$new[i])
# eb1S <- UpdateSeuratObject(eb1S)
# save(eb1S,file=filemap$v2[i])
# }
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
load(sub("old.RData","savedRes.RData",filemap$old[i]))
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- data_for_scClustViz$cl[names(temp_cells),savedRes,drop=F]
rownames(temp_cl) <- temp_cells
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_seur <- subset(temp_seur,cells=temp_cells)
[email protected] <- pDat[temp_cells,]
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
for (i in 1:5) {
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
load(sub("old.RData","savedRes.RData",filemap$old[i]))
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_cl <- getMD(temp_seur)[,savedRes,drop=F]
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
}
load("~/MK_MSN/MouseSciaticNerve/inst/InjCombined/InjCombined.RData")
names(InjCombined_sCVdL)
library(scClustViz)
length(DEvsRest(InjCombined_sCVdL))
length(DEvsRest(InjCombined_sCVdL$res.1.6))
HumanLiver::viewHumanLiver()
length(DEvsRest(sCVdL))
length(DEvsRest(sCVdL$res.0.8))
sapply(DEvsRest(sCVdL$res.0.8),dim)
sapply(DEvsRest(InjCombined_sCVdL$res.1.6),dim)
sapply(DEcombn(sCVdL$res.0.8),dim)
sapply(DEcombn(InjCombined_sCVdL$res.1.6),dim)
length(DEcombn(InjCombined_sCVdL$res.1.6))
length(DEcombn(sCVdL$res.0.8))
InjCombined_seur@assays
InjCombined_seur@graphs
InjCombined_seur@neighbors
InjCombined_seur
InjCombined_seur@assays$RNA@counts
InjCombined_seur@assays$RNA@data
InjCombined_seur@assays$RNA@counts < 0
InjCombined_seur@assays$RNA@data< 0
sum(InjCombined_seur@assays$RNA@data < 0)
temp_seur <- InjCombined_seur
temp_seur@assays$RNA@data[temp_seur@assays$RNA@data < 0] <- 0
load(filemap$old[i])
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
# for (i in 1:6) {
# load(filemap$new[i])
# eb1S <- UpdateSeuratObject(eb1S)
# save(eb1S,file=filemap$v2[i])
# }
i <- 6
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
load(sub("old.RData","savedRes.RData",filemap$old[i]))
temp_cells <- sapply(colnames(data_for_scClustViz$nge),function(X) grep(X,colnames(getExpr(eb1S)),value=T))
temp_cl <- data_for_scClustViz$cl[names(temp_cells),,drop=F]
# temp_cl <- data_for_scClustViz$cl[names(temp_cells),savedRes,drop=F]
rownames(temp_cl) <- temp_cells
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_seur@assays$RNA@data[temp_seur@assays$RNA@data < 0] <- 0
temp_seur <- subset(temp_seur,cells=temp_cells)
[email protected] <- pDat[temp_cells,]
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
for (i in 1:5) {
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
load(filemap$new[i])
load(filemap$v2[i])
load(filemap$old[i])
load(sub("old.RData","savedRes.RData",filemap$old[i]))
temp_seur <- DietSeurat(UpdateSeuratObject(eb1S),counts=F)
temp_seur@assays$RNA@data[temp_seur@assays$RNA@data < 0] <- 0
temp_cl <- data_for_scClustViz$cl[names(temp_cells),,drop=F]
# temp_cl <- getMD(temp_seur)[,savedRes,drop=F]
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
assign(paste(temp_name,"seur",sep="_"),temp_seur)
assign(paste(temp_name,"sCVdL",sep="_"),temp_scv)
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
}
i
temp_name
temp_cl <- data_for_scClustViz$cl
# temp_cl <- getMD(temp_seur)[,savedRes,drop=F]
if (all(rownames(pDat) == rownames(getMD(temp_seur)))) {
[email protected] <- pDat
} else {
stop("rownames don't line up")
}
temp_scv <- CalcAllSCV(inD=temp_seur,clusterDF=temp_cl,assayType="RNA")
head(temp_cl)
savedRes
source('~/MK_MSN/MouseSciaticNerve/R/temp_makenew.R', echo=TRUE)
library(scClustViz)
library(Seurat)
filemap <- data.frame(old=c("inst/Inj9dBeads/Inj9dBeads_old.RData",
"inst/Inj9dBeadsMesenchymal/Inj9dBeadsMesenchymal_old.RData",
"inst/Inj9dFACS/Inj9dFACS_old.RData",
"inst/InjCombined/InjCombined_old.RData",
"inst/InjUninjMesenchymalCombined/InjUninjMesenchymalCombined_old.RData",
"inst/UninjMesenchymal/UninjMesenchymal_old.RData"),
new=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S.RData"),
v2=c("../MouseSciaticNerve_eb1S/9dInjuredBeads/9dInjuredBeads_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredBeadsMesenchymal/9dInjuredBeadsMesenchymal_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/9dInjuredFACS/9dInjuredFACS_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/CombinedInjured/CombinedInjured_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombined/InjUninjMesCombined_eb1S_v2.RData",
"../MouseSciaticNerve_eb1S/InjUninjMesCombinedBatchCorrected/InjUninjMesCombinedBatchCorrected_eb1S_v2.RData"),
stringsAsFactors=F)
i <- 1
load("~/MK_MSN/MouseSciaticNerve/inst/Inj9dBeads/Inj9dBeads.RData")
load("~/MK_MSN/MouseSciaticNerve/inst/Inj9dBeads/Inj9dBeads_savedRes.RData")
sapply(Inj9dBeads_sCVdL,function(X) length(levels(Clusters(X))))
temp_sCV <- Inj9dBeads_sCVdL[1:2]
Inj9dBeads_sCVdL <- temp_sCV
temp_name <- strsplit(filemap$old[i],"/",fixed=T)[[1]][2]
paste(temp_name,"seur",sep="_")
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
Inj9dBeads_sCVdL <- temp_sCV["res.3.2"]
save(list=c(paste(temp_name,"seur",sep="_"),paste(temp_name,"sCVdL",sep="_")),
file=paste0("inst/",temp_name,"/",temp_name,".RData"))
q("no")