Completado procesado de datos de Checkpoint Inhibitors.

BDAccess/app.R

@@ -9,6 +9,9 @@ library(openCyto)
 library(flowCore)
 library(flowWorkspace)
 library(CytoML)
+library(ggcyto)
+
+filter<-dplyr::filter
 
 print(getwd())
 source("../sqlFunctions.R", encoding = "UTF-8")
@@ -73,7 +76,8 @@ ui <- fluidPage(
             mainPanel(
                 htmlOutput("report"),
                 h3("Nitrogen"),
-                tableOutput("nitrogen")
+                tableOutput("nitrogen"),
+                plotOutput("visorplot")
             )
         ),
 
@@ -83,13 +87,20 @@ ui <- fluidPage(
                      selectInput("phenotype", "Tipo de análisis", selected="Pop", choices=c("Pop", "IC")),
                  ),
                  mainPanel(
-                     actionButton("goButtonDir","Selecciona directorio fenotipo"),
-                     textOutput("session"),
-                     hr(),
-                     actionButton("fcsconvert", "Convertir a fcs"),
-                     hr(),
-                     actionButton("pngexport", "Exportar informes"),
-                     actionButton("popexport", "Actualizar BBDD")
+                     tabsetPanel(
+                         tabPanel("Entrada",
+                             actionButton("goButtonDir","Selecciona directorio fenotipo"),
+                             textOutput("session"),
+                             hr(),
+                             actionButton("fcsconvert", "Convertir a fcs"),
+                             hr(),
+                             actionButton("pngexport", "Exportar informes"),
+                             actionButton("popexport", "Actualizar BBDD")
+                        ),
+                        tabPanel("Visor",
+
+                        )
+                     )
                  )
         ),
 
@@ -843,50 +854,128 @@ server <- function(input, output) {
     })
     
     observeEvent(input$pngexport,{
-        route<-cito_dir
-
-        ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
-        gs<-flowjo_to_gatingset(ws, name="All Samples")
-        
-        sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% 
-            gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
-        
-        for (samp in sampleNames(gs)){
-            print(samp)
-            p<-autoplot(gs[[samp]], bins=64)
-            ggsave(paste0(route, samp,".png"),p,width = 10, height = 10)
+        if (input$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$phenotype == "IC"){
+            route<-cito_dir
+            
+            ws<-open_flowjo_xml(paste0(route,"IC.wsp"))
+            gs<-flowjo_to_gatingset(ws, name="All Samples")
+            
+            sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% 
+                gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
+            
+            names<-sampleNames(gs) %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique()
+            
+            nodes<-gs_get_pop_paths(gs)
+            nodes_parent<-nodes[!grepl("CTLA4|LAG3|PD1|TIGIT|TIM3|root$", nodes)]
+            nodes_cd4<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD4/",nodes)]
+            nodes_cd8<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD8/",nodes)]
+            
+            for (id in names){
+                print(id)
+                iso<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("iso",sampleNames(gs))]
+                ab<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("ab",sampleNames(gs))]
+                
+                g1<-ggcyto_arrange(autoplot(gs[[ab]], nodes_parent, bins=128), nrow=1)
+                g2<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd8, bins=64), nrow=1)
+                g3<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd8, bins=64), nrow=1)
+                g4<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd4, bins=64), nrow=1)
+                g5<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd4, bins=64), nrow=1)
+                g_all<-gridExtra::gtable_rbind(g1,g2,g3,g4,g5)
+                ggsave(paste0(route,id,".IC.png"), g_all, width = 10, height = 10)
+            }
+        }
     })
-    
-    observeEvent(input$popexport,{
-        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)
         
-        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)
-        
-        pop[,"pop"]<-gsub("_","",pop$pop)
-        pop$pop<-gsub(" ","_",pop$pop)
-        pop$pop<-gsub("+","pos",pop$pop, fixed=T)
-        pop$pop<-gsub("-","neg",pop$pop, fixed=T)
-        pop<-rename(pop, "samples"="sample")
-        pop$percent<-round(pop$percent, digits=2)
-        pop_sp<-pop %>% spread(pop, percent)
-        
-        vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length)
-        names(vartypes)<-pop_sp %>% select(-samples) %>% colnames
-        
-        sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F)
-        print("Tabla POPULATIONS sincronizada.")
-        
-    })
+    observeEvent(input$popexport,{
+        if (input$phenotype == "Pop"){
+            route<-cito_dir
+            
+            ws<-open_flowjo_xml(paste0(route,"Populations.wsp"))
+            gs<-flowjo_to_gatingset(ws, name="All Samples")
+            
+            sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% 
+                gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
+            
+            nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1)
+            nodes<-nodes[grepl("_",nodes)]
+            pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100)
+            
+            pop[,"pop"]<-gsub("_","",pop$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")
+            pop$percent<-round(pop$percent, digits=2)
+            pop_sp<-pop %>% spread(pop, percent)
+            
+            vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length)
+            names(vartypes)<-pop_sp %>% select(-samples) %>% colnames
+            
+            sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F)
+            print("Tabla POPULATIONS sincronizada.")
+        }
+        if (input$phenotype == "IC"){
+            route<-cito_dir
+            
+            ws<-open_flowjo_xml(paste0(route,"IC.wsp"))
+            gs<-flowjo_to_gatingset(ws, name="All Samples")
+            
+            sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% 
+                gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T)
+            
+            nodes<-gs_get_pop_paths(gs)
+            # nodes<-gsub("â\u0081»", "-", nodes)
+            # nodes<-gsub("â\u0081º", "+", nodes)
+            nodes<-nodes[grepl("CTLA4", nodes)]
+            nodes<-nodes[!grepl("CD4$|CD8$|CTLA4$|TIM3$|PD1$|LAG3$|TIGIT$|/CTLA4â\u0081»$|/TIM3â\u0081»$|/PD1â\u0081»$|/LAG3â\u0081»$|/TIGITâ\u0081»$", nodes)]
+            
+            pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100)
+            pop$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(" ", "_", pop$pop)
+            
+            pop["Type"]<-"ab"
+            pop[grepl("iso|ISO|Iso",pop$sample),"Type"]<-"iso"
+            pop$sample<-gsub("iso|ISO|Iso|ab|AB|Ab| ","",pop$sample)
+            
+            pop_sp<-pop %>% spread(Type, percent)
+            pop_sp["Net"]<-pop_sp$ab
+            pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"Net"]<-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"ab"]-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"iso"]
+            pop_sp$Net[pop_sp$Net < 0]<-0
+            pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/","",.)
+            pop_sp$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) %>% 
+                gather(pop, value, -sample,-Population) %>% summarise(n=100-sum(value)) %>% pull(n)
+            pop_sp <- rename(pop_sp, "samples"="sample")
+            
+            vartypes<-rep("Number", pop_sp %>% select(-samples, -Population) %>% colnames %>% length)
+            names(vartypes)<-pop_sp %>% select(-samples, -Population) %>% colnames
+            
+            sqlSave(dta, pop_sp, tablename="IC", append = T, varTypes = vartypes, rownames = F)
+            print("Tabla IC sincronizada.")
+        }
+    }) 
+
 
 ## scRNAseq ----