From 20bf1d2c2003c756db5d7b402dca24dfcec2c87a Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Mon, 4 Apr 2022 17:30:55 +0200
Subject: [PATCH] =?UTF-8?q?He=20a=C3=B1adido=20al=20visor=20de=20muestras?=
 =?UTF-8?q?=20el=20plot=20de=20IC.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 BDAccess/app.R | 34 ++++++++++++++++++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/BDAccess/app.R b/BDAccess/app.R
index a6f38ee..130d65e 100644
--- a/BDAccess/app.R
+++ b/BDAccess/app.R
@@ -77,7 +77,7 @@ ui <- fluidPage(
                 htmlOutput("report"),
                 h3("Nitrogen"),
                 tableOutput("nitrogen"),
-                plotOutput("visorplot")
+                plotOutput("visorplot", height = "1000px")
             )
         ),
 
@@ -831,7 +831,7 @@ server <- function(input, output) {
         if (input$nhc == 3){
             pops<-sqlFetch(dta, "POPULATIONS")
             
-            pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
+            g_pop<-pops %>% dplyr::filter(samples == input$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"))) %>% 
                 ggplot(aes(pop, value))+
@@ -839,6 +839,36 @@ server <- function(input, output) {
                     labs(title = input$id, y="% parent", x="")+
                     theme_bw()+
                     theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5))
+            tl<-sqlFetch(dta, "IC") %>% filter(samples == input$id)
+            
+            mtl<-melt(tl, variable.name = "Receptors")
+            mtl$Receptors<-as.character(mtl$Receptors) #Para poder depurar bien el texto, lo pasamos a tipo character
+            mtl$Receptors<-gsub("n","-",mtl$Receptors, fixed = T)
+            mtl$Receptors<-gsub("p","+",mtl$Receptors, fixed = T)
+            mtl$Receptors<-gsub("_"," ",mtl$Receptors)
+            mtl[mtl$value < 1, "Receptors"]<-"Other"
+            mtl$Receptors<-gsub("[A-Z]*-*[0-9T]- *", "", mtl$Receptors)
+            mtl$Receptors<-gsub("+ $", "", mtl$Receptors)
+            mtl$Receptors[mtl$Receptors == ""]<-"All Negative"
+            
+            mtl$Receptors<-factor(mtl$Receptors)
+            mtl$Population<-factor(mtl$Population, levels = c("CD8", "CD4"))
+            
+            # colorCount<-length(unique(mtl$Receptors))
+            # getPalette = colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))
+            
+            color<-c(c("CTLA4+ LAG3+ PD1+ TIGIT+ TIM3+"="black","All Negative"="white","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E","TIGIT+"="#FA7055"),
+                     c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F","PD1+ TIGIT+"="#D259AA", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "CTLA4+ TIGIT+"="#9C929A", "LAG3+ TIM3+"="#9ED848", "TIGIT+ TIM3+"="#ACB353", "LAG3+ TIGIT+"="#EC964A"),
+                     c("CTLA4+ PD1+ TIGIT+"="#B86B6A","CTLA4+ PD1+ TIGIT+ TIM3+"="#B81515","LAG3+ PD1+ TIGIT+"="#007D8A", "PD1+ TIGIT+ TIM3+"="#D64545", "LAG3+ PD1+ TIGIT+ TIM3+"="#0f5860", "LAG3+ TIGIT+ TIM3+"="#50cad3"))
+            
+            g_IC<-ggplot(mtl, aes(samples, value, fill=Receptors))+
+                geom_bar(stat="summary", fun="sum",color="black")+
+                labs(x="Patient", y="% CD8+", fill="")+
+                facet_grid(.~Population)+
+                scale_fill_manual(values = color[levels(mtl$Receptors)[levels(mtl$Receptors) %in% unique(mtl$Receptors)]])+
+                theme_bw()+
+                theme(axis.text.x=element_text(angle=45, hjust=1))
+            ggpubr::ggarrange(g_pop, g_IC, heights = c(0.4, 0.6), ncol = 1)
         }
     })