fixed too small font size in metrices plot. Additionally, the combine…

…d data is also displayed for parameter and metrices for the batch process
ComPlat · Aug 21, 2024 · cb86baf · cb86baf
1 parent 120ec10
commit cb86baf
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diff --git a/Tests/Batch/Rplots.pdf b/Tests/Batch/Rplots.pdf
diff --git a/Tests/Batch/plotting.R b/Tests/Batch/plotting.R
@@ -0,0 +1,86 @@
+l <- readRDS("/home/konrad/Documents/GitHub/RProjects/Thermosimfit/Tests/Batch/res_batch.rds")
+
+plotMetrices <- function(list, num_rep = 1) {
+  list <- list[[3]]
+  num_data_sets <- length(list) / num_rep
+  repetitions <- (seq_len(length(list)) - 1) %% num_rep + 1
+  data_sets <- rep(1:num_data_sets, each = num_rep)
+  for (i in seq_along(list)) {
+    list[[i]]$dataset <- data_sets[i]
+    list[[i]]$repetition <- repetitions[i]
+  }
+  df <- Reduce(rbind, list)
+  data <- data.frame(
+    x = rep(df[, 6], 5),
+    y = c(df[, 1], df[, 2], df[, 3], df[, 4], df[, 5]),
+    names = c(
+      rep(names(df)[1], nrow(df)),
+      rep(names(df)[2], nrow(df)),
+      rep(names(df)[3], nrow(df)),
+      rep(names(df)[4], nrow(df)),
+      rep(names(df)[5], nrow(df))
+    ),
+    repetition = rep(df$repetition, 5)
+  )
+  base_size <- 14
+  if (num_rep > 1) {
+    p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          y = y, fill = "Entire data", x = factor(0)
+        )
+      ) +
+      geom_boxplot(
+        data = data,
+        aes(
+          x = factor(x), y = y,
+          group = factor(x),
+          fill = factor(x)
+        )
+      ) +
+      facet_wrap(. ~ names,
+        scales = "free_y",
+        strip.position = "left"
+      ) +
+      xlab(NULL) +
+      ylab(NULL) +
+      theme(
+        strip.background = element_blank(),
+        strip.placement = "outside"
+      ) +
+      guides(fill = guide_legend(title = "Datasets"))
+  } else {
+    p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          x = factor(x),
+          y = y,
+          group = names
+        )
+      ) +
+      facet_wrap(~names,
+        scales = "free_y",
+        strip.position = "left"
+      ) +
+      xlab(NULL) +
+      ylab(NULL) +
+      theme(
+        strip.background = element_blank(),
+        strip.placement = "outside"
+      )
+  }
+  p <- p + theme(
+    legend.position = "bottom",
+    axis.title = element_text(size = base_size * 1.2, face = "bold"),
+    axis.text = element_text(size = base_size, face = "bold"),
+    legend.text = element_text(size = base_size),
+    legend.title = element_text(size = base_size),
+    strip.text.x = element_text(size = base_size * 1.2, face = "bold"),
+    strip.text.y = element_text(size = base_size * 1.2, face = "bold")
+  )
+  return(p)
+}
+library(ggplot2)
+plotMetrices(l, 2)
diff --git a/Tests/Batch/res_batch.rds b/Tests/Batch/res_batch.rds
diff --git a/Tests/Batch/test.R b/Tests/Batch/test.R
@@ -9,133 +9,6 @@ res_batch <- tsf:::batch(
   additionalParameters = c(host = 1.00E-06, dye = 1.00E-06, kHD = 3.00E+06),
   ngen = 20, num_rep = 2
 )
+# saveRDS(res_batch[[1]], "res_batch.rds")
 
-plotStates <- function(list, num_rep = 1) {
-  list <- list[[1]]
-  num_data_sets <- length(list) / num_rep
-  repetitions <- (seq_len(length(list)) - 1) %% num_rep + 1
-  data_sets <- rep(1:num_data_sets, each = num_rep)
-  for (i in seq_along(list)) {
-    list[[i]]$dataset <- data_sets[i]
-    list[[i]]$repetition <- repetitions[i]
-  }
-  df <- Reduce(rbind, list)
-  # dye and host dye plot
-  data <- data.frame(
-    x = rep(df[, 1], 2),
-    y = c(df[, 4], df[, 5]),
-    names = c(
-      rep(names(df)[4], nrow(df)),
-      rep(names(df)[5], nrow(df))
-    ),
-    repetition = rep(df$repetition, 2),
-    dataset = rep(df$dataset, 2)
-  )
-  base_size <- 14
-  if (num_rep > 1) {
-    xlabels <- as.character(unique(rbind(df[, 1], "")))
-    xlabels[(seq_along(xlabels) %% 10) != 1] <- ""
-    p <- ggplot() +
-      geom_boxplot(
-        data = data,
-        aes(
-          x = interaction(dataset, x), y = y,
-          fill = factor(dataset),
-          group = interaction(dataset, x)
-        ),
-        width = 0.25,
-        size = 0.25
-      ) +
-      facet_wrap(. ~ names,
-        strip.position = "left",
-        scales = "free_y"
-      ) +
-      xlab(names(df)[1]) +
-      ylab(NULL) +
-      guides(fill = guide_legend(title = "Datasets")) +
-      scale_x_discrete(
-        labels = xlabels
-      )
-  } else {
-    p <- ggplot() +
-      geom_boxplot(
-        data = data,
-        aes(
-          x = x,
-          y = y,
-          group = factor(x)
-        )
-      ) +
-      facet_wrap(~names,
-        strip.position = "left",
-        scales = "free_y"
-      ) +
-      ylab(NULL) +
-      xlab(names(df)[1])
-  }
-  p <- p + theme(
-    legend.position = "bottom",
-    axis.title = element_text(size = base_size * 1.2, face = "bold"),
-    axis.text = element_text(size = base_size),
-    legend.text = element_text(size = base_size),
-    legend.title = element_text(size = base_size),
-    strip.text.x = element_text(size = base_size * 1.2, face = "bold"),
-    strip.text.y = element_text(size = base_size * 1.2, face = "bold"),
-    axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
-  )
-  # signal plot
-  data_signal_measured <- data.frame(
-    x = c(df[, 1], df[, 1]),
-    y = c(df[, 2], df[, 3]),
-    names = c(
-      rep(names(df)[2], nrow(df)),
-      rep(names(df)[3], nrow(df))
-    ),
-    repetition = rep(df$repetition, 2),
-    dataset = rep(df$dataset, 2)
-  )
-
-  xlevels <- levels(factor(data_signal_measured$x))
-  xlabels <- xlevels
-  xlabels[(seq_along(xlevels) %% 3) != 1] <- ""
-  p_signal <- ggplot(
-    data = data_signal_measured,
-    aes(
-      x = factor(x),
-      y = y,
-      colour = factor(dataset),
-      group = interaction(x, dataset, repetition)
-    )
-  ) +
-    geom_point(
-      data = subset(data_signal_measured, names != "Signal measured"),
-      aes(shape = factor(repetition))
-    ) +
-    geom_smooth(
-      data = subset(data_signal_measured, names == "Signal measured"),
-      aes(x = factor(x), y = y, group = 1, colour = "Measured")
-    ) +
-    scale_x_discrete(labels = xlabels) +
-    xlab(names(df)[1]) +
-    ylab(NULL) +
-    theme(
-      legend.position = "bottom",
-      axis.title = element_text(size = base_size * 1.2, face = "bold"),
-      axis.text = element_text(size = base_size),
-      legend.text = element_text(size = base_size),
-      legend.title = element_text(size = base_size),
-      strip.text.x = element_text(size = base_size, face = "bold"),
-      strip.text.y = element_text(size = base_size * 1.2, face = "bold"),
-      axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
-    ) +
-    guides(
-      shape = guide_legend(title = "Repetitions"),
-      colour = guide_legend(title = "Datasets")
-    )
-  return(list(p_signal, p))
-}
-
-library(ggplot2)
-
-plotStates(res_batch[[1]], 2)[[1]]
-plotStates(res_batch[[1]], 2)[[2]]
+res_batch
diff --git a/stdout b/stdout
diff --git a/tsf/R/Batch.R b/tsf/R/Batch.R
@@ -250,6 +250,12 @@ plotParams <- function(list, num_rep = 1) {
   base_size <- 14
   if (num_rep > 1) {
     p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          y = y, fill = "Entire data", x = factor(0)
+        )
+      ) +
       geom_boxplot(
         data = data,
         aes(
@@ -302,7 +308,6 @@ plotParams <- function(list, num_rep = 1) {
   return(p)
 }
 
-# TODO: metrices increase label size
 plotMetrices <- function(list, num_rep = 1) {
   list <- list[[3]]
   num_data_sets <- length(list) / num_rep
@@ -328,6 +333,12 @@ plotMetrices <- function(list, num_rep = 1) {
   base_size <- 14
   if (num_rep > 1) {
     p <- ggplot() +
+      geom_boxplot(
+        data = data,
+        aes(
+          y = y, fill = "Entire data", x = factor(0)
+        )
+      ) +
       geom_boxplot(
         data = data,
         aes(
@@ -371,14 +382,16 @@ plotMetrices <- function(list, num_rep = 1) {
   p <- p + theme(
     legend.position = "bottom",
     axis.title = element_text(size = base_size * 1.2, face = "bold"),
-    axis.text = element_text(size = base_size),
+    axis.text = element_text(size = base_size, face = "bold"),
     legend.text = element_text(size = base_size),
     legend.title = element_text(size = base_size),
-    strip.text.x = element_text(size = base_size)
+    strip.text.x = element_text(size = base_size * 1.2, face = "bold"),
+    strip.text.y = element_text(size = base_size * 1.2, face = "bold")
   )
   return(p)
 }
 
+
 batch <- function(case,
                   lowerBounds, upperBounds,
                   path,

diff --git a/tsf/Rplots.pdf b/tsf/Rplots.pdf