changing heatmap color gradient

.Rbuildignore

@@ -10,3 +10,4 @@ $run_dev.*
 ^appveyor\.yml$
 ^cran-comments\.md$
 ^\.github$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.7.0
+Date: 2023-04-26 14:46:04 UTC
+SHA: 47a6512dd7df6e86075b3247994562e3bd39e449

R/heatmap_VICI.R

@@ -18,6 +18,7 @@
 heatmap_vici <- function(res_2plot, inter=TRUE, baseline=NULL){
 
   if(inter){
+
     p <- ggplot(data = res_2plot) +
       geom_tile(aes_string(x="Stimulation", y="response", fill="pvalue"), color="white") +
       theme_minimal() +
@@ -26,11 +27,11 @@ heatmap_vici <- function(res_2plot, inter=TRUE, baseline=NULL){
               subtitle = "taking into account background response levels") +
       labs(caption = "made with VICI") +
       ylab("ICS response") +
-      scale_fill_manual(values = c("red4", "red2", "coral2", "grey70", "grey75", "grey80", "grey85","grey90", "grey95"),
-                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)"),
-                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.2[", "[0.2,0.3[", "[0.3,0.4[", "[0.4,0.5[", "[0.5,1]"),
+      scale_fill_manual(values = c("red4", "red3", "coral2", "grey80", "grey90", "grey95"),
+                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.5)", "[0.5,1)"),
+                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.5[", "[0.5,1]"),
                         name="P-value",
-                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)")
+                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.5)", "[0.5,1)")
       ) + facet_wrap(c("Arm"), labeller = "label_both")
   }else{
     p <- ggplot(data = res_2plot) +
@@ -41,13 +42,13 @@ heatmap_vici <- function(res_2plot, inter=TRUE, baseline=NULL){
               subtitle = "taking into account background response levels") +
       labs(caption = "made with VICI") +
       ylab("ICS response") +
-      scale_fill_manual(values = c("red4", "red2", "coral2", "grey70", "grey75", "grey80", "grey85","grey90", "grey95"),
-                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)"),
-                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.2[", "[0.2,0.3[", "[0.3,0.4[", "[0.4,0.5[", "[0.5,1]"),
+      scale_fill_manual(values = c("red4", "red3", "coral2", "grey80", "grey90", "grey95"),
+                        breaks = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.5)", "[0.5,1)"),
+                        labels = c("[0,0.001[", "[0.001,0.01[", "[0.01,0.05[", "[0.05,0.1[", "[0.1,0.5[", "[0.5,1]"),
                         name="P-value",
-                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.2)", "[0.2,0.3)", "[0.3,0.4)", "[0.4,0.5)", "[0.5,1)")
+                        limits = c("[0,0.001)", "[0.001,0.01)", "[0.01,0.05)", "[0.05,0.1)", "[0.1,0.5)", "[0.5,1)")
       ) + facet_wrap(c("Timepoint"), labeller = "label_both")
   }
-
+  
   return(p)
 }

R/mod_modelfit.R

@@ -88,7 +88,7 @@ mod_modelfit_server <- function(input, output, session, datas,parent,origin){
             heatmap_data2plot[[response]] <- responses_res[[response]]$postprocess_res$res_2plot
             heatmap_data2plot[[response]]$response <- response
             heatmap_data2plot[[response]]$pvalue <- cut(heatmap_data2plot[[response]]$pvalue,
-                                                        breaks = c(0, 0.001, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 1),
+                                                        breaks = c(0, 0.001, 0.01, 0.05, 0.1, 0.5, 1),
                                                         right = FALSE)
             responses_res[[response]]$res_tab <- fit_res$res_tab
 
@@ -156,7 +156,7 @@ mod_modelfit_server <- function(input, output, session, datas,parent,origin){
               for(l in 1:length(heatmap_data2plot[[response]])){
                 heatmap_data2plot[[response]][[l]]$response <- response
                 heatmap_data2plot[[response]][[l]]$pvalue <- cut(heatmap_data2plot[[response]][[l]]$pvalue,
-                                                                 breaks = c(0, 0.001, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 1),
+                                                                 breaks = c(0, 0.001, 0.01, 0.05, 0.1, 0.5, 1),
                                                                  right = FALSE)
               }
               heatmap_data2plot[[response]] <- do.call(rbind.data.frame,