|
|
@ -1079,17 +1079,47 @@ server <- function(input, output) { |
|
|
|
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% |
|
|
|
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
|
|
|
|
|
|
|
bool.comb<-apply( |
|
|
|
expand.grid(c("","!"), c("","!"),c("","!"), c("","!"), c("","!")), |
|
|
|
1, |
|
|
|
function(x) paste0(x[1],"CTLA4 & ",x[2],"LAG3 & ",x[3],"PD1 & ",x[4], "TIGIT & ",x[5], "TIM3") |
|
|
|
) |
|
|
|
|
|
|
|
bool.name<-apply( |
|
|
|
expand.grid(c("+","-"), c("+","-"),c("+","-"), c("+","-"), c("+","-")), |
|
|
|
1, |
|
|
|
function(x) paste0("CTLA4",x[1]," LAG3",x[2]," PD1",x[3]," TIGIT",x[4]," TIM3",x[5]) |
|
|
|
) |
|
|
|
|
|
|
|
for (i in 1:length(bool.comb)){ |
|
|
|
print("Booleanos CD8") |
|
|
|
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) |
|
|
|
boolgate<-eval(call) |
|
|
|
gs_pop_add(gs, boolgate, parent="CD8", name = bool.name[i]) |
|
|
|
} |
|
|
|
|
|
|
|
for (i in 1:length(bool.comb)){ |
|
|
|
print("Booleanos CD4") |
|
|
|
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) |
|
|
|
boolgate<-eval(call) |
|
|
|
gs_pop_add(gs, boolgate, parent="CD4", name = bool.name[i]) |
|
|
|
} |
|
|
|
|
|
|
|
recompute(gs) |
|
|
|
|
|
|
|
nodes<-gs_get_pop_paths(gs) |
|
|
|
# nodes<-gsub("â\u0081»", "-", nodes) |
|
|
|
# nodes<-gsub("â\u0081º", "+", nodes) |
|
|
|
nodes<-nodes[grepl("CTLA4", nodes)] |
|
|
|
nodes<-nodes[!grepl("CD4$|CD8$|CTLA4$|TIM3$|PD1$|LAG3$|TIGIT$|/CTLA4â\u0081»$|/TIM3â\u0081»$|/PD1â\u0081»$|/LAG3â\u0081»$|/TIGITâ\u0081»$", nodes)] |
|
|
|
nodes<-nodes[!grepl("CD4$|CD8$|CTLA4$|TIM3$|PD1$|LAG3$|TIGIT$", nodes)] |
|
|
|
|
|
|
|
pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) |
|
|
|
pop$percent<-round(pop$percent, digits=2) |
|
|
|
|
|
|
|
pop$pop<-gsub("â\u0081»", "n", pop$pop) |
|
|
|
pop$pop<-gsub("â\u0081º", "p", pop$pop) |
|
|
|
# pop$pop<-gsub("â\u0081»", "n", pop$pop) |
|
|
|
# pop$pop<-gsub("â\u0081º", "p", pop$pop) |
|
|
|
pop$pop<-gsub("-", "n", pop$pop, fixed=T) |
|
|
|
pop$pop<-gsub("+", "p", pop$pop, fixed=T) |
|
|
|
pop$pop<-gsub(" ", "_", pop$pop) |
|
|
|
|
|
|
|
pop["Type"]<-"ab" |
|
|
@ -1104,10 +1134,13 @@ server <- function(input, output) { |
|
|
|
pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) |
|
|
|
|
|
|
|
pop_sp<-pop_sp %>% select(-ab,-iso) %>% spread(pop,Net) |
|
|
|
pop_sp$`CTLA4n_LAG3n_PD1n_TIGITn_TIM3n`<- pop_sp %>% select(-`CTLA4n_LAG3n_PD1n_TIGITn_TIM3n`) %>% group_by(sample,Population) %>% |
|
|
|
pop_sp$CTLA4n_LAG3n_PD1n_TIGITn_TIM3n<- pop_sp %>% select(-CTLA4n_LAG3n_PD1n_TIGITn_TIM3n) %>% group_by(sample,Population) %>% |
|
|
|
gather(pop, value, -sample,-Population) %>% summarise(n=100-sum(value)) %>% pull(n) |
|
|
|
pop_sp <- rename(pop_sp, "samples"="sample") |
|
|
|
|
|
|
|
pop_sql<-sqlFetch(dta, "IC") %>% slice(0) |
|
|
|
pop_sp<-pop_sp %>% merge(pop_sql, all=T) %>% select(colnames(pop_sql)) |
|
|
|
|
|
|
|
vartypes<-rep("Number", pop_sp %>% select(-samples, -Population) %>% colnames %>% length) |
|
|
|
names(vartypes)<-pop_sp %>% select(-samples, -Population) %>% colnames |
|
|
|
|
|
|
|