refactoring update boxplot

sistm · Feb 2, 2024 · 0b2cadf · 0b2cadf
1 parent babf5a6
commit 0b2cadf
Showing 1 changed file with 27 additions and 54 deletions.
diff --git a/R/boxplot_VICI.R b/R/boxplot_VICI.R
@@ -8,6 +8,8 @@
 #'Default is \code{TRUE}.
 #'@param baseline baseline value used in title when \code{inter} is \code{FALSE}.
 #'Default is \code{NULL}.
+#'@param fill a logical flag indicating if the boxplot is filled
+#'Default if \code{FALSE}
 #'
 #'@return a \code{ggpubr} plot object
 #'
@@ -19,75 +21,46 @@
 #'@import ggpubr
 #'@import RColorBrewer
 
-boxplot_VICI <- function(data_df, pval_2plot, response_name, input, inter=TRUE, baseline=NULL){
+boxplot_VICI <- function(data_df, pval_2plot, response_name, input, inter=TRUE, baseline=NULL,fill=FALSE){
 
+  if(!is.numeric(data_df$response)){
+    data_df$response <- as.numeric(data_df$response)
+  }
 
   p <- NULL
+
   if(inter){
     data_df$arm <- relevel(data_df$arm, ref=input$selectRefArmInter)
     suppressWarnings(
       if(input$jiter == "None"){
-        p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", palette = "RdGy",
-                       alpha=0.3,)+
-          theme_classic() +
-          theme(panel.grid.major.x = element_blank()) +
-          scale_color_brewer(palette = input$color) +
-          stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
-                             tip.length = 0.025) +
-          ylab(paste0("Response ", response_name)) +
-          xlab("Stimulation") +
-          ggtitle(paste0("Arm effect on ", response_name),
-                  subtitle = "p-values taking into account background response levels through bivariate modeling") +
-          labs(caption = "made with VICI")
+        p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", 
+                       palette = "RdGy", fill = "stim", alpha=0.3)
       }else{
-      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", palette = "RdGy",
-                  alpha=0.3,
-                  add="jitter",
-                  shape = as.numeric(input$jiter))+
-        theme_classic() +
-        theme(panel.grid.major.x = element_blank()) +
-        scale_color_brewer(palette = input$color) +
-        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
-                           tip.length = 0.025) +
-        ylab(paste0("Response ", response_name)) +
-        xlab("Stimulation") +
-        ggtitle(paste0("Arm effect on ", response_name),
-                subtitle = "p-values taking into account background response levels through bivariate modeling") +
-        labs(caption = "made with VICI")
-      },
+        p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "arm", palette = "RdGy",fill = "stim",
+                       alpha=0.3, add="jitter", shape = as.numeric(input$jiter))
+      }
     )
   }else{
     data_df$time <- relevel(data_df$time, ref=input$selectRefTimeIntra)
+
     if(input$jiter == "None"){
-      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "time", palette = "RdGy",
-                     alpha=0.3,) + 
-        theme_classic() +
-        theme(panel.grid.major.x = element_blank()) +
-        scale_color_brewer(palette = input$color)+
-        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
-                           tip.length =  0.025) +
-        ylab(paste0("Response ", response_name)) +
-        xlab("Stimulation") +
-        ggtitle(paste0("Intra-arm vaccine effect on ", response_name, " compared to baseline ", baseline),
-                subtitle = "p-values taking into account background response levels through bivariate modeling") +
-        labs(caption = "made with VICI")
+      p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "time", palette = "RdGy", alpha=0.3)
     }else{
       p <- ggboxplot(na.omit(data_df), x="stim", y="response", color= "time", palette = "RdGy",
-                     alpha=0.3,
-                     add="jitter",
-                     shape = as.numeric(input$jiter))+
-        theme_classic() +
-        theme(panel.grid.major.x = element_blank()) +
-        scale_color_brewer(palette = input$color)+
-        stat_pvalue_manual(data = pval_2plot, label = "pvalue_format",
-                           tip.length =  0.025) +
-        ylab(paste0("Response ", response_name)) +
-        xlab("Stimulation") +
-        ggtitle(paste0("Intra-arm vaccine effect on ", response_name, " compared to baseline ", baseline),
-                subtitle = "p-values taking into account background response levels through bivariate modeling") +
-        labs(caption = "made with VICI")
+                     alpha=0.3, add="jitter", shape = as.numeric(input$jiter))
     }
   }
+
+  p <- p + theme_grey() + 
+    theme(panel.grid.major.x = element_blank()) +
+    scale_color_brewer(palette = input$color) +
+    stat_pvalue_manual(data = pval_2plot, label = "pvalue_format", tip.length = 0.025) +
+    ylab(paste0("Response ", response_name)) +
+    xlab("Stimulation") +
+    ggtitle(paste0("Arm effect on ", response_name),
+            subtitle = "p-values taking into account background response levels through bivariate modeling") +
+    labs(caption = "made with VICI")
+
   return(p)
-
+  
 }