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CitoProccess
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Añadido el código para el panel3.

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marcelcosta 2 years ago
parent
5ce8a61b8e
commit
3dfae26144
1 changed files with 246 additions and 36 deletions
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  1. +246
    -36
      CitoProcess/app.R

+ 246
- 36
CitoProcess/app.R
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@ -4,6 +4,7 @@ library(flowCore)
library(flowWorkspace)
library(CytoML)
library(ggcyto)
library(RColorBrewer)
# library(reshape2)
# library(CitFuns)
library(openxlsx)
@ -82,21 +83,6 @@ server <- function(input, output) {
})
observeEvent(input$pngexport,{
# if (input$phenotype == "Pop"){
# route<-cito_dir
#
# ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
# gs<-flowjo_to_gatingset(ws, name="All Samples")
#
# sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>%
# gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
#
# for (samp in sampleNames(gs)){
# print(samp)
# p<-autoplot(gs[[samp]], bins=64)
# ggsave(paste0(route, samp,".pop.png"),p,width = 10, height = 10)
# }
# }
if (input$phenotype == "Panel1"){
route<-cito_dir
@ -278,39 +264,186 @@ server <- function(input, output) {
}
print("Informes finalizados!")
}
})
observeEvent(input$popexport,{
if (input$phenotype == "Pop"){
if (input$phenotype == "Panel3"){
route<-cito_dir
ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
ws<-open_flowjo_xml(paste0(route,"Panel3.wsp"))
gs<-flowjo_to_gatingset(ws, name="All Samples")
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>%
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Panel3 ")[[1]][2]) %>%
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1)
nodes<-nodes[grepl("_",nodes)]
pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100)
gs<-gs[sampleNames(gs)[!grepl("Iso|ISO|iso|NoBV421",sampleNames(gs))]]
pop[,"pop"]<-gsub("_","",pop$pop)
pop$pop<-gsub(" ","_",pop$pop)
pop$pop<-gsub("+","pos",pop$pop, fixed=T)
pop$pop<-gsub("-","neg",pop$pop, fixed=T)
pop<-rename(pop, "samples"="sample")
bool.comb<-apply(
expand.grid(c("","!"), c("","!"), c("","!")),
1,
function(x) paste0(x[1],"CD38 & ",x[2],"HLADR & ",x[3],"GZMB")
)
bool.name<-apply(
expand.grid(c("+","-"), c("+","-"), c("+","-")),
1,
function(x) paste0("CD38",x[1]," HLADR",x[2]," GZMB",x[3])
)
print("Booleanos CD8")
for (i in 1:length(bool.comb)){
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i])))
boolgate<-eval(call)
gs_pop_add(gs, boolgate, parent="CD8", name = bool.name[i])
}
print("Booleanos CD4")
for (i in 1:length(bool.comb)){
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i])))
boolgate<-eval(call)
gs_pop_add(gs, boolgate, parent="CD4", name = bool.name[i])
}
print("Booleanos NK")
for (i in 1:length(bool.comb)){
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i])))
boolgate<-eval(call)
gs_pop_add(gs, boolgate, parent="NK", name = bool.name[i])
}
recompute(gs)
names<-sampleNames(gs) # %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique()
nodes<-gs_get_pop_paths(gs)
# nodes<-gsub("â\u0081»", "-", nodes)
# nodes<-gsub("â\u0081º", "+", nodes)
nodes<-nodes[grepl("CD38", nodes)]
nodes<-nodes[!grepl("CD38$|HLADR$|GZMB$", 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_sp<-pop %>% spread(pop, percent)
pop_sql<-sqlFetch(dta, "POPULATIONS") %>% slice(0)
pop_sp<-pop_sp %>% merge(pop_sql, all=T) %>% select(colnames(pop_sql))
# 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)
## Esto si no hay isotipo
pop_sp<-pop
pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/|_","",.)
pop_sp$Population[is.na(pop_sp$Population)]<-"NK"
pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1)
pop_sp<-pop_sp %>% spread(pop, percent)
vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length)
names(vartypes)<-pop_sp %>% select(-samples) %>% colnames
pop_sql<-read.xlsx(paste0(db_path,"Panel3.xlsx"), check.names = F, sep.names = " ")
pop_sp<-pop_sp %>% merge(pop_sql %>% slice(0), all=T) %>% select(colnames(pop_sql))
sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F)
print("Tabla POPULATIONS sincronizada.")
for (id in names){
print(id)
data<-pop_sp %>% filter(sample == id)
data1<-data %>% gather(phen, value, -sample, -Population)
# data1$phen<-gsub("p","+",data1$phen)
# data1$phen<-gsub("n","-",data1$phen)
# data1$phen<-gsub("_"," ",data1$phen)
# data1$phen<-gsub("n","-",data1$phen, fixed = T)
# data1$phen<-gsub("p","+",data1$phen, fixed = T)
# data1$phen<-gsub("_"," ",data1$phen)
# data1[data1$value < 1, "phen"]<-"Other"
data1$phen<-gsub("[A-Z0-9]*-", "", data1$phen)
data1$phen<-gsub(" ", " ", data1$phen)
data1$phen<-gsub("[ ]*$", "", data1$phen)
data1$phen<-gsub("^[ ]*", "", data1$phen)
data1$phen[data1$phen == ""]<-"All Negative"
data1["phen1"]<-"CD38"
data1[!grepl("CD38+", data1$phen),"phen1"]<-NA
data1["phen2"]<-"HLADR"
data1[!grepl("HLADR+", data1$phen),"phen2"]<-NA
data1["phen3"]<-"GZMB"
data1[!grepl("GZMB+", data1$phen),"phen3"]<-NA
data1<-data1 %>% arrange(desc(value))
data2<-data1 %>% filter(!phen %in% c("All Negative","Other"))
data1<-rbind(data2, data1 %>% filter(phen %in% c("All Negative","Other")) %>% arrange(desc(phen)))
data_cd8<-data1 %>% filter(Population == "CD8")
data_cd4<-data1 %>% filter(Population == "CD4")
data_NK<-data1 %>% filter(Population == "NK")
data_cd8$ymax<-cumsum(data_cd8$value)
data_cd8$ymin<-c(0, head(data_cd8$ymax, n=-1))
data_cd4$ymax<-cumsum(data_cd4$value)
data_cd4$ymin<-c(0, head(data_cd4$ymax, n=-1))
data_NK$ymax<-cumsum(data_NK$value)
data_NK$ymin<-c(0, head(data_NK$ymax, n=-1))
data1<-rbind(data_cd8, data_cd4, data_NK)
# color<-c(c("CTLA4+ LAG3+ PD1+ TIM3+"="black","All Negative"="grey90","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E"),
# c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "LAG3+ TIM3+"="#9ED848"),
# c("CTLA4+ PD1+ TIM3+"="#B81515", "LAG3+ PD1+ TIM3+"="#0f5860"))
# basic.color<-color[c("PD1+","TIM3+","CTLA4+","LAG3+")]
# names(basic.color)<-c("PD1","TIM3","CTLA4","LAG3")
# Make the plot
color<-colorRampPalette(brewer.pal(8, "Set3"))(length(bool.name))
names(color)<-bool.name %>% gsub("[A-Z0-9]*-", "", .) %>% gsub(" "," ",.) %>% gsub("[ ]*$", "", .) %>% gsub("^[ ]*", "", .) %>% gsub("^$","All Negative", .)
color["All Negative"]<-"grey90"
basic.color<-color[c("CD38+","HLADR+","GZMB+")]
names(basic.color)<-c("CD38","HLADR","GZMB")
g_coex<-ggplot(data1)+
facet_grid(.~factor(Population, levels=c("CD8","CD4","NK")))+
geom_rect(aes(ymax=ymax, ymin=ymin, xmax=4.5, xmin=0), fill=color[data1$phen])+
geom_rect(aes(ymax=ymax, ymin=ymin, xmax=5.4, xmin=5, fill=factor(phen1, levels=c("CD38","HLADR","GZMB"))))+
geom_rect(aes(ymax=ymax, ymin=ymin, xmax=5.9, xmin=5.5, fill=factor(phen2, levels=c("CD38","HLADR","GZMB"))))+
geom_rect(aes(ymax=ymax, ymin=ymin, xmax=6.4, xmin=6, fill=factor(phen3, levels=c("CD38","HLADR","GZMB"))))+
scale_fill_manual(values = basic.color, na.value="#FFFFFF00", drop=F, limits=c("CD38","HLADR","GZMB"), name="Activation")+
coord_polar(theta="y") + # Try to remove that to understand how the chart is built initially
xlim(c(0, 6.5)) +# Try to remove that to see how to make a pie chart
theme_classic()+
theme(strip.background = element_blank(),
strip.text = element_text(size=12, face="bold"),
axis.line = element_blank(),
axis.ticks = element_blank(),
# plot.margin = margin(-200,0,0,0),
axis.text = element_blank())
nodes<-gs_get_pop_paths(gs)
nodes_parent<-nodes[!grepl("CD38|HLADR|GZMB|root$", nodes)]
nodes_cd4<-nodes[grepl("CD38$|HLADR$|GZMB$", nodes) & grepl("/CD4/",nodes)]
nodes_cd8<-nodes[grepl("CD38$|HLADR$|GZMB$", nodes) & grepl("/CD8/",nodes)]
nodes_NK<-nodes[grepl("CD38$|HLADR$|GZMB$", nodes) & grepl("/NK/",nodes)]
g1<-ggcyto_arrange(autoplot(gs[[id]], nodes_parent), nrow=3)
g2<-ggcyto_arrange(autoplot(gs[[id]], nodes_cd8), nrow=1)
g3<-ggcyto_arrange(autoplot(gs[[id]], nodes_cd4), nrow=1)
g4<-ggcyto_arrange(autoplot(gs[[id]], nodes_NK), nrow=1)
g_dots<-ggpubr::ggarrange(gridExtra::gtable_rbind(g1), NULL,
gridExtra::gtable_rbind(g2,g3,g4), nrow=1, widths=c(0.35,0.1,0.55))
# g_dots<-gridExtra::gtable_cbind(g1, gridExtra::gtable_rbind(g2,g3,g4))
g_all<-ggpubr::ggarrange(g_dots, g_coex, ncol=1, heights=c(0.75,0.25))
ggsave(paste0(route,id,".Panel3.png"), g_all, width = 14, height = 12)
ggsave(paste0(db_path, "Informes/",id,".Panel3.png"), g_all, width = 14, height = 12)
}
print("Informes finalizados!")
}
})
observeEvent(input$popexport,{
if (input$phenotype == "Panel1"){
route<-cito_dir
@ -427,6 +560,83 @@ server <- function(input, output) {
write.xlsx(list("IC"=ic_sp, "POPULATIONS"=pop_sp), paste0(db_path, "Panel1.xlsx"))
print("Tabla Panel1 sincronizada.")
}
if (input$phenotype == "Panel3"){
route<-cito_dir
ws<-open_flowjo_xml(paste0(route,"Panel3.wsp"))
gs<-flowjo_to_gatingset(ws, name="All Samples")
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Panel3 ")[[1]][2]) %>%
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
gs<-gs[sampleNames(gs)[!grepl("Iso|ISO|iso|NoBV421",sampleNames(gs))]]
bool.comb<-apply(
expand.grid(c("","!"), c("","!"), c("","!")),
1,
function(x) paste0(x[1],"CD38 & ",x[2],"HLADR & ",x[3],"GZMB")
)
bool.name<-apply(
expand.grid(c("+","-"), c("+","-"), c("+","-")),
1,
function(x) paste0("CD38",x[1]," HLADR",x[2]," GZMB",x[3])
)
print("Booleanos CD8")
for (i in 1:length(bool.comb)){
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])
}
print("Booleanos CD4")
for (i in 1:length(bool.comb)){
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])
}
print("Booleanos NK")
for (i in 1:length(bool.comb)){
call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i])))
boolgate<-eval(call)
gs_pop_add(gs, boolgate, parent="NK", name = bool.name[i])
}
recompute(gs)
names<-sampleNames(gs) # %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique()
nodes<-gs_get_pop_paths(gs)
# nodes<-gsub("â\u0081»", "-", nodes)
# nodes<-gsub("â\u0081º", "+", nodes)
nodes<-nodes[grepl("CD38", nodes)]
nodes<-nodes[!grepl("CD38$|HLADR$|GZMB$", nodes)]
pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100)
pop$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("-", "n", pop$pop, fixed=T)
# pop$pop<-gsub("+", "p", pop$pop, fixed=T)
# pop$pop<-gsub(" ", "_", pop$pop)
## Esto si no hay isotipo
pop_sp<-pop
pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/|_","",.)
pop_sp$Population[is.na(pop_sp$Population)]<-"NK"
pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1)
pop_sp<-pop_sp %>% spread(pop, percent)
pop_sql<-read.xlsx(paste0(db_path,"Panel3.xlsx"), check.names = F, sep.names = " ")
pop_sp<-pop_sp %>% merge(pop_sql %>% slice(0), all=T) %>% select(colnames(pop_sql))
write.xlsx(pop_sp, paste0(db_path, "Panel3.xlsx"))
print("Tabla Panel3 sincronizada.")
}
})
}

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