Commit in cytometry.

BDAccess/app.R

@@ -88,6 +88,7 @@ ui <- fluidPage(
                      tabsetPanel(
                          tabPanel("Entrada",
                              actionButton("goButtonDir","Selecciona directorio fenotipo"),
+                             textInput("cytopath", label="Directorio fenotipo", value=""),
                              textOutput("session"),
                              hr(),
                              actionButton("fcsconvert", "Convertir a fcs"),
@@ -143,24 +144,28 @@ server <- function(input, output) {
         print(CCfile)
         if (input$dbtype == "UM"){
             dta<<-odbcConnectAccess2007(access.file = UMfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         if (input$dbtype == "OV"){
             dta<<-odbcConnectAccess2007(access.file = OVfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         if (input$dbtype == "CC"){
             dta<<-odbcConnectAccess2007(access.file = CCfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         print(dta)
         if (input$backup == T){
             if (! input$dbtype %in% c("UM","OV")){
-                sqlBackUp(bu.dir="CC_BU")
-            }else{
-                sqlBackUp()   
+                sqlBackUp(dbfile = CCfile, bu.dir="CC_BU")
             }
-                
+            if (input$dbtype == "UM"){
+              sqlBackUp(dbfile = UMfile)
+            }
+            if (input$dbtype == "OV"){
+                sqlBackUp(dbfile = OVfile)
+            }
+            print("Back up realizado.")   
         }
     })
     
@@ -379,7 +384,7 @@ server <- function(input, output) {
             new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "samples"=new.samp) %>% merge(sqlFetch(dta,"OVID"), all.x=T) %>% arrange(samples)
             samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
             if (today==TRUE){
-                samples.exp$IQ_date<-format(Sys.Date(), "%d/%m/%y")
+                samples.exp$Date_extraction<-format(Sys.Date(), "%d/%m/%y")
             }
             
             nhc.table<-values[["DF"]]
@@ -753,6 +758,7 @@ server <- function(input, output) {
                 sqlFetch(dta, "NITROGEN"),
                 file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","UM-Nitrogen.xlsx")
             )
+            print("Backup Creado.")
             
             table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
             
@@ -783,6 +789,7 @@ server <- function(input, output) {
             
             sqlDrop(dta, "NITROGEN")
             sqlSave(dta, table.um %>% select(-FECHA) %>% filter(!is.na(CODIGO)), tablename="NITROGEN", rownames=F)
+            print("Tabla Actualizada.")
         }
         if (input$dbtype == "OV"){
             ## Copia de backup
@@ -796,6 +803,7 @@ server <- function(input, output) {
                 sqlFetch(dta, "NITROGEN"),
                 file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","OV-Nitrogen.xlsx")
             )
+            print("Backup Creado.")
             
             ## Lectura del excel
             table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
@@ -821,6 +829,7 @@ server <- function(input, output) {
             
             sqlDrop(dta, "NITROGEN")
             sqlSave(dta, table.ov, tablename="NITROGEN", rownames=F)
+            print("Tabla Actualizada.")
         }
 
     })
@@ -923,9 +932,14 @@ server <- function(input, output) {
             
             pops<-sqlFetch(dta, "POPULATIONS")
             
-            g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
-                mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
-                                                "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+            g_pop<-pops %>% 
+              dplyr::filter(sample == input$id) %>% 
+              gather(pop,value,-sample, -code, -fc_time) %>%
+                # mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
+                #                                 "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+              # mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
+                                              # "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+                mutate(value=as.numeric(gsub(",",".",value))) %>% 
                 ggplot(aes(pop, value))+
                     geom_bar(stat="identity", color="black", fill="grey70")+
                     labs(title = input$id, y="% parent", x="")+
@@ -969,7 +983,11 @@ server <- function(input, output) {
 
     observe({
         if(input$goButtonDir > 0){
+            if (input$cytopath == ""){
                 cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/")
+            }else{
+                cito_dir<<-input$cytopath %>% gsub("\\","/",. ,fixed=T) %>% gsub("/$", "", .) %>% paste0("/")
+            }
 
             output$session <- renderText(
                     cito_dir
@@ -1008,7 +1026,7 @@ server <- function(input, output) {
         }
         
         if (input$phenotype == "IC"){
-            route<-cito_dir
+            route<-stringi::stri_enc_tonative(cito_dir)
 
             ws<-open_flowjo_xml(paste0(route,"IC.wsp"))
             gs<-flowjo_to_gatingset(ws, name="All Samples")
@@ -1169,6 +1187,11 @@ server <- function(input, output) {
                           # plot.margin = margin(-200,0,0,0),
                           axis.text = element_blank())
                 
+                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)]
+                
                 # 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)