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Merge pull request #220 from PNNL-CompBio/dev
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updating cell type matching
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@sgosline
sgosline committed Sep 11, 2023
2 parents 175770e + 008a863 commit d7b07d8
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Showing 2 changed files with 30 additions and 25 deletions.
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55 changes: 30 additions & 25 deletions simulatedData/mapSimDataMatrices.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,12 @@ main <- function(){
stringr::str_replace('DC$','Dendritic cells')%>%
stringr::str_replace(fixed('T cells CD4'),'CD4 T cells')%>%
stringr::str_replace('Eosinophil$','Eosinophils')%>%
stringr::str_replace(fixed('T cells CD4 naive'),'CD4 naive T-cells')%>%
stringr::str_replace(fixed('T cells CD4 memory activated'),'CD4 memory T-cells activated')%>%
stringr::str_replace(fixed('T cells CD4 memory resting'),'CD4 memory T-cells resting')
stringr::str_replace(fixed('T cells CD4 naive'),'CD4 naive T cells')%>%
stringr::str_replace(fixed('T cells CD4 memory activated'),'CD4 memory T cells activated')%>%
stringr::str_replace(fixed('T cells CD4 memory resting'),'CD4 memory T cells resting')|>
stringr::str_replace(fixed('CD4 T cells naive'),'CD4 naive T cells')%>%
stringr::str_replace(fixed('CD4 T cells memory activated'),'CD4 memory T cells activated')%>%
stringr::str_replace(fixed('CD4 T cells memory resting'),'CD4 memory T cells resting')

##now let's get the cell types to use the same nomenclature
rownames(cell.type)<-rownames(cell.type)%>%
Expand All @@ -57,9 +60,10 @@ main <- function(){
stringr::str_replace('^NK$','NK cells')%>%
stringr::str_replace(fixed('B cells naive'),'Naive B cells')%>%
stringr::str_replace(fixed('B cells memory'),'Memory B cells')%>%
stringr::str_replace(fixed('T cells CD4 naive'),'CD4 naive T-cells')%>%
stringr::str_replace(fixed('T cells CD4 memory activated'),'CD4 memory T-cells activated')

stringr::str_replace(fixed('T cells CD4 naive'),'CD4 T cells naive')%>%
stringr::str_replace(fixed('T cells CD4 memory activated'),'CD4 memory T cells activated')|>
stringr::str_replace(fixed('T cells CD4 memory resting'),'CD4 memory T cells resting')


##massive if-else clause to match cell types :-/
if(sig.mat=='LM9.txt'){
Expand All @@ -69,32 +73,33 @@ main <- function(){
}else if(sim.type=='mrna'){
#do nothing
}else if(sim.type=='pbmc'){
cell.type['CD4 T cells',]<-cell.type['CD4 naive T-cells',]+
cell.type['CD4 memory T-cells resting',]+
cell.type['CD4 memory T-cells activated',]
cell.type['CD4 T cells',]<-cell.type['CD4 naive T cells',]+
cell.type['CD4 memory T cells resting',]+
cell.type['CD4 memory T cells activated',]
cell.type['B cells',]<-cell.type['Naive B cells',]+
cell.type['Memory B cells',]
}
}else if(sig.mat=='LM22.txt'){
#can convert to any other
if(sim.type=='prot'){
##fix t8 cells
deconv.mat['B cells',]<-deconv.mat['B cells naive',]+
deconv.mat['B cells memory',]
deconv.mat['CD4 T cells',]<- deconv.mat['T cells CD4 naive',]+
deconv.mat['T cells CD4 memory activated',]+
deconv.mat['T cells CD4 memory resting',]
deconv.mat['B cells',]<-deconv.mat['Naive B cells',]+
deconv.mat['Memory B cells',]
deconv.mat['CD4 T cells',]<- deconv.mat['CD4 naive T-cells',]+
deconv.mat['CD4 memory T-cells activated',]+
deconv.mat['CD4 memory T-cells resting',]
deconv.mat['NK cells',]<-deconv.mat['NK cells activated',]+
deconv.mat['NK cells resting',]
deconv.mat['Dendritic cells',]<-deconv.mat['Dendritic cells activated',]+
deconv.mat['Dendritic cells resting',]

}else if(sim.type=='mrna'){
deconv.mat['B cells',]<-deconv.mat['B cells naive',]+
deconv.mat['B cells memory',]
deconv.mat['CD4 T cells',]<- deconv.mat['T cells CD4 naive',]+
deconv.mat['T cells CD4 memory activated',]+
deconv.mat['T cells CD4 memory resting',]
deconv.mat['B cells',]<-deconv.mat['Naive B cells',]+
deconv.mat['Memory B cells',]
deconv.mat['CD4 T cells',]<- deconv.mat['CD4 naive T cells',]+
deconv.mat['CD4 memory T cells activated',]+
deconv.mat['CD4 memory T cells resting',]
deconv.mat['T cells CD4 memory resting',]
deconv.mat['NK cells',]<-deconv.mat['NK cells activated',]+
deconv.mat['NK cells resting',]
}else if(sim.type=='pbmc'){
Expand All @@ -111,9 +116,9 @@ main <- function(){
}else if(sim.type=='mrna'){
#do nothing
}else if(sim.type=='pbmc'){
cell.type['CD4 T cells',]<-cell.type['CD4 naive T-cells',]+
cell.type['CD4 memory T-cells resting',]+
cell.type['CD4 memory T-cells activated',]
cell.type['CD4 T cells',]<-cell.type['CD4 naive T cells',]+
cell.type['CD4 memory T cells resting',]+
cell.type['CD4 memory T cells activated',]
cell.type['B cells',]<-cell.type['Naive B cells',]+
cell.type['Memory B cells',]

Expand All @@ -125,9 +130,9 @@ main <- function(){
}else if(sim.type=='mrna'){
#do nothing
}else if(sim.type=='pbmc'){
cell.type['CD4 T cells',]<-cell.type['CD4 naive T-cells',]+
cell.type['CD4 memory T-cells resting',]+
cell.type['CD4 memory T-cells activated',]
cell.type['CD4 T cells',]<-cell.type['CD4 naive T cells',]+
cell.type['CD4 memory T cells resting',]+
cell.type['CD4 memory T cells activated',]

cell.type['B cells',]<-cell.type['Naive B cells',]+
cell.type['Memory B cells',]
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