Functional Update

R/confidence_plot.groups.R

@@ -0,0 +1,41 @@
+overconfidence_plot.groups <- function(data, color = blue, plot = "jitter", colorbg = blue202, name = "", export = FALSE, group) {
+
+  require(ggplot2)
+  require(ggpubr)
+  require(RColorBrewer)
+
+  df <- data.frame(Score = data, Class = "", Group = group)
+
+  if(plot == "jitter") {
+
+    bxp <- ggplot(df, aes(y = Score, color = Group, x = Group), ylim = c(0,1)) +
+      geom_hline(yintercept = c(0.2,0.5, 0.8), color = "black", size = 0.5, linetype = "dashed") +
+      geom_hline(yintercept = c(0,1), color = "black", size = 0.5, linetype="dashed") + 
+      geom_violin(aes(fill = Group), width = 0.8)  + 
+      geom_boxplot(width=0.4, position = position_dodge(width=0.9), )+ 
+      scale_color_manual(values = c("black", "black", "black"))+
+      scale_fill_manual(values = c(rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95)), name = "")+
+      theme(strip.text.y = element_text(angle = 0), 
+            axis.ticks.x = element_blank()) 
+
+    bxp1 <- bxp + theme_pubr()+ 
+      theme(legend.position = "none", axis.ticks.x = element_blank()) + 
+      xlab("")+
+      ylab("Overconfidence Score")+
+      scale_y_continuous(breaks = c(0, 0.2, 0.5, 0.8, 1), limits = c(0,1)) + 
+      guides(fill=guide_legend(title=""), color = "none")  +
+      geom_jitter(color=color, size=3, alpha=0.5, width = 0.25)
+
+  } 
+
+  if (export == TRUE) {
+    name <- paste(name,".pdf", sep = "")
+    ggsave(name, bxp1, width = 10, height = 6)
+  }
+
+  return(bxp1)
+
+
+}

R/miscalibration_plot.groups.R

@@ -0,0 +1,34 @@
+miscalibration_plot.groups <- function(miscalibration, calibrationaccuracy, 
+                                         export = FALSE, name = "", group) {
+
+  require(ggplot2)
+  require(ggpubr)
+  require(RColorBrewer)
+
+  grey95 <- rgb(0.95, 0.95, 0.95)
+
+  dfx <- data.frame(Score = miscalibration, Class = "", accuracy = calibrationaccuracy, Group = group)
+
+  t1 <- ggplot(dfx, aes(x = Group, y = Score), ylim = c(-1,1)) +
+    geom_hline(yintercept = 0, color = "black", size = 0.5, linetype = "dashed")+
+    geom_violin(aes(fill = Group), fill = grey95) +#facet_wrap(~Group)+
+    geom_boxplot(width = 0.3) +
+    geom_jitter(width = 0.25, size = 3, aes(color = accuracy), alpha = 0.9)+
+    scale_color_gradient(low = "red", high = green, limits = c(0,1), 
+                         name = "Calibration    \nAccuracy\n") + 
+    theme_pubr(legend = "right")+
+    xlab("")+
+    scale_y_continuous(breaks = c(-1, -0.5, 0, 0.5, 1), limits = c(-1, 1))+
+    ylab("Miscalibration Score")+
+    theme(strip.text.y = element_text(angle = 0), axis.ticks.x = element_blank()) 
+
+
+  if (export == TRUE) {
+    name <- paste(name,".pdf", sep = "")
+    ggsave(name, t1, width = 10, height = 6)
+  }
+
+
+  return(t1)
+
+}

R/overconfidence_plot.groups.R

@@ -0,0 +1,41 @@
+overconfidence_plot.groups <- function(data, color = blue, plot = "jitter", colorbg = blue202, name = "", export = FALSE, group) {
+
+  require(ggplot2)
+  require(ggpubr)
+  require(RColorBrewer)
+
+  df <- data.frame(Score = data, Class = "", Group = group)
+
+  if(plot == "jitter") {
+
+    bxp <- ggplot(df, aes(y = Score, color = Group, x = Group), ylim = c(0,1)) +
+      geom_hline(yintercept = c(0.2,0.5, 0.8), color = "black", size = 0.5, linetype = "dashed") +
+      geom_hline(yintercept = c(0,1), color = "black", size = 0.5, linetype="dashed") + 
+      geom_violin(aes(fill = Group), width = 0.8)  + 
+      geom_boxplot(width=0.4, position = position_dodge(width=0.9), )+ 
+      scale_color_manual(values = c("black", "black", "black"))+
+      scale_fill_manual(values = c(rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95)), name = "")+
+      theme(strip.text.y = element_text(angle = 0), 
+            axis.ticks.x = element_blank()) 
+
+    bxp1 <- bxp + theme_pubr()+ 
+      theme(legend.position = "none", axis.ticks.x = element_blank()) + 
+      xlab("")+
+      ylab("Overconfidence Score")+
+      scale_y_continuous(breaks = c(0, 0.2, 0.5, 0.8, 1), limits = c(0,1)) + 
+      guides(fill=guide_legend(title=""), color = "none")  +
+      geom_jitter(color=color, size=3, alpha=0.5, width = 0.25)
+
+  } 
+
+  if (export == TRUE) {
+    name <- paste(name,".pdf", sep = "")
+    ggsave(name, bxp1, width = 10, height = 6)
+  }
+
+  return(bxp1)
+
+
+}

R/underconfidence_plot.groups.R

@@ -0,0 +1,41 @@
+underconfidence_plot.groups <- function(data, color = blue, plot = "jitter", colorbg = blue202, name = "", export = FALSE, group) {
+
+  require(ggplot2)
+  require(ggpubr)
+  require(RColorBrewer)
+
+  df <- data.frame(Score = data, Class = "", Group = group)
+
+  if(plot == "jitter") {
+
+    bxp <- ggplot(df, aes(y = Score, color = Group, x = Group), ylim = c(0,1)) +
+      geom_hline(yintercept = c(0.2,0.5, 0.8), color = "black", size = 0.5, linetype = "dashed") +
+      geom_hline(yintercept = c(0,1), color = "black", size = 0.5, linetype="dashed") + 
+      geom_violin(aes(fill = Group), width = 0.8)  + 
+      geom_boxplot(width=0.4, position = position_dodge(width=0.9), )+ 
+      scale_color_manual(values = c("black", "black", "black"))+
+      scale_fill_manual(values = c(rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95), 
+                                   rgb(0.95, 0.95, 0.95)), name = "")+
+      theme(strip.text.y = element_text(angle = 0), 
+            axis.ticks.x = element_blank()) 
+
+    bxp1 <- bxp + theme_pubr()+ 
+      theme(legend.position = "none", axis.ticks.x = element_blank()) + 
+      xlab("")+
+      ylab("Underconfidence Score")+
+      scale_y_continuous(breaks = c(0, 0.2, 0.5, 0.8, 1), limits = c(0,1)) + 
+      guides(fill=guide_legend(title=""), color = "none")  +
+      geom_jitter(color=color, size=3, alpha=0.5, width = 0.25)
+
+  } 
+
+  if (export == TRUE) {
+    name <- paste(name,".pdf", sep = "")
+    ggsave(name, bxp1, width = 10, height = 6)
+  }
+
+  return(bxp1)
+
+
+}