slight updates to figures

Author: sgosline

manuscript/coderdataResultsFunctions.R

@@ -138,10 +138,12 @@ calcSourceStatistics<-function(metric, dataset=cdres){
     left_join(stats) |>
     arrange(meanVal)
 
-  mom <- gres|> group_by(src,Combos)|> summarize(mv = mean(meanVal))|> arrange(mv)
+ # mom <- gres|>
+#    group_by(src,Combos)|>
+#    summarize(mv = mean(meanVal))|>
+#    arrange(mv)
 
-  #gres <- subset(gres,met=='scc')
-  gres$src = factor(gres$src,levels = unique(mom$src))
+#  gres$src = factor(gres$src,levels = unique(mom$src))
 
   p1 <- ggplot(gres, aes(x=Samples, y = meanVal,col=model))+
     geom_point()+scale_x_log10()+scale_color_manual(values=modelcolors)+geom_smooth(method=lm, alpha=0.2)+theme_bw()
@@ -161,7 +163,7 @@ calcSourceStatistics<-function(metric, dataset=cdres){
   p4 <- ggplot(corvals, aes(x=statistic,y=correlation,fill=model)) + geom_bar(position='dodge',stat='identity') +
     scale_fill_manual(values=modelcolors) + theme_bw()
 
-  return(cowplot::plot_grid(p1,p2,p3,p4,nrow=2))
+  return(cowplot::plot_grid(p1,p2,p3,p4,nrow=4))
 }
 
 ##do we still need this function?

manuscript/figure4ExVivoResults.Rmd

@@ -5,11 +5,7 @@ date: "2025-06-02"
 output: html_document
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-Here we are focused on getting the details from a model prediction algorithm - where did it fail, where did it succeed?
+This figure focuses on the ex vivo results
 
 ## Data and packages
 
@@ -39,7 +35,7 @@ The data has been uploaded by natasha and can be downloaded as follows.
 
 ```{r}
 exres = lapply(metrics,function(x) {
-  doFullPlot(x, ecdres,'cellline')
+  ridgelineMetricPlots(x, ecdres,'cellline')
   })
 
 print(exres)
@@ -54,6 +50,7 @@ plot<-calcSourceStatistics('scc',ecdres)
 
 
 ggsave('exVivoSamplePerformanceCorrelation.pdf',plot, height=12)
+print(plot)
 
 ```