Merge pull request #13 from giovannellilab/dev

Merge dev branch changes for perimeter/area calculation and mean polygon

DESCRIPTION

@@ -14,7 +14,7 @@ Authors@R: c(
     person("Donato", "Giovannelli", role = "aut",
            email = "donato.giovannelli@unina.it"))
 Description: Polygon plot is designed to visualize multivariate ranges as opposite to single data points and it is able to show 3 to 6 variables simultaneously showcase the min-max and average for each.
-License: CC BY-SA 4.0
+License: CC BY-SA 4.0 + file LICENSE
 URL: https://github.com/giovannellilab/polygonPlot
 BugReports: https://github.com/giovannellilab/polygonPlot/issues
 Encoding: UTF-8
@@ -23,7 +23,9 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Imports:
     checkmate,
-    ggplot2
+    ggplot2,
+    dplyr,
+    pracma
 Suggests:
     knitr,
     RefManageR,

NAMESPACE

@@ -4,4 +4,7 @@ export(overlay_polygons)
 export(polygonplot)
 export(prepare_dataframe)
 import(checkmate)
+import(dplyr)
 import(ggplot2)
+importFrom(pracma,polyarea)
+importFrom(stats,dist)

R/hexagon.R

@@ -348,5 +348,13 @@
       }
   }
 
+  # Add mean polygon
+  p = p + .draw_mean_polygon(df_coord)
+
+  # Print perimeter and area
+  message(sprintf("Perimeter: %5.2f", .get_perimeter(df_coord)))
+  message(sprintf("Area:      %5.2f", .get_area(df_coord)))
+
+
   return(p)
 }

R/mean-polygon.R

@@ -0,0 +1,58 @@
+#' Calculates the mean coordinates for further plotting the mean polygon
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return A data.frame with the mean coordinates.
+#' 
+#' @examples
+#' .get_mean_coords(data.frame(x=c(8, 8, 22, 24), y=c(12, 15, 8, 8)))
+#' 
+#' @seealso [polygonPlot::.get_perimeter()]
+#' 
+#' @import dplyr
+.get_mean_coords = function(df) {
+
+  mean_df = data.frame()
+
+  # WARNING: this code assumes the order of the points is correct!
+  for (i in seq(from=1, to=nrow(df), by=2)) {
+    mean_df = mean_df %>%
+      bind_rows(
+        df %>% slice(i, i+1) %>% summarise(x=mean(x), y=mean(y))
+      )
+  }
+
+  return(mean_df)
+}
+
+#' Plots the mean polygon
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return The mean polygon as a `ggplot2` object.
+#' 
+#' @examples
+#' .draw_mean_polygon(data.frame(x=c(8, 8, 22, 24), y=c(12, 15, 8, 8)))
+#' 
+#' @seealso [polygonPlot::.get_perimeter()]
+#' 
+#' @import checkmate
+#' @import ggplot2
+.draw_mean_polygon = function(df) {
+  checkmate::assertDataFrame(x=df, col.names="named", ncols=2)
+
+  # Get mean coordinates from original ones
+  mean_df = .get_mean_coords(df)
+
+  p = ggplot2::geom_polygon(
+      data=mean_df,
+      aes(x=x, y=y),
+      fill="darkgrey",
+      colour="darkgrey",
+      alpha=0.0,
+      linetype=1,
+      linewidth=0.5
+    )
+
+  return(p)
+}

R/overlay_polygons.R

@@ -11,6 +11,7 @@
 #'
 #' @import checkmate
 #' @import ggplot2
+
 overlay_polygons <- function(plot_list, label_list, matching_color_points=FALSE) {
   checkmate::assertList(plot_list, types = "ggplot")
   checkmate::assertCharacter(label_list, len = length(plot_list), 

R/pentagon.R

@@ -296,6 +296,13 @@
                                      angle=288)
       }
   }
+
+  # Add mean polygon
+  p = p + .draw_mean_polygon(df_coord)
+
+  # Print perimeter and area
+  message(sprintf("Perimeter: %5.2f", .get_perimeter(df_coord)))
+  message(sprintf("Area:      %5.2f", .get_area(df_coord)))
 
   return(p)
 }

R/square.R

@@ -234,5 +234,12 @@
       }
   }
 
+  # Add mean polygon
+  p = p + .draw_mean_polygon(df_coord)
+
+  # Print perimeter and area
+  message(sprintf("Perimeter: %5.2f", .get_perimeter(df_coord)))
+  message(sprintf("Area:      %5.2f", .get_area(df_coord)))
+
   return(p)
 }

R/triangle.R

@@ -187,6 +187,13 @@
                                  label=tick, size=3.5, angle=60)
     }
   }
+
+  # Add mean polygon
+  p = p + .draw_mean_polygon(df_coord)
+
+  # Print perimeter and area
+  message(sprintf("Perimeter: %5.2f", .get_perimeter(df_coord)))
+  message(sprintf("Area:      %5.2f", .get_area(df_coord)))
 
   return(p)
 }

R/util.R

@@ -34,3 +34,88 @@ prepare_dataframe <- function(dataframe){
 
   return(m)
 }
+
+#' Calculates the length of each side of the polygon
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return The list of lengths as a numeric vector.
+#' 
+#' @seealso [polygonPlot::.get_perimeter()]
+#' 
+#' @importFrom stats dist
+#' @import checkmate
+.get_lengths = function(df) {
+  checkmate::assertDataFrame(x=df, col.names="named", ncols=2)
+
+  len_list = c()
+
+  # WARNING: this code assumes the order of the points is correct!
+  # Get the points for each axis 2 by 2 (corresponding to each side)
+  for (i in seq(from=1, to=nrow(df), by=2)) {
+    len_list = c(len_list, stats::dist(df[i:(i+1),]))
+  }
+
+  return(len_list)
+}
+
+#' Calculates the perimeter of the polygon
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return The perimeter as numeric.
+#' 
+#' @seealso [polygonPlot::.get_area()]
+#' 
+#' @import checkmate
+.get_perimeter = function(df) {
+  checkmate::assertDataFrame(x=df, col.names="named", ncols=2)
+
+  return(sum(.get_lengths(df)))
+}
+
+#' Collapses the original polygon by linking each segment to the last vertex
+#' of the previous segment, basically connecting all sides to the base.
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return The coordinates of the collapsed polygon as a data frame.
+#' 
+#' @seealso [polygonPlot::.get_area()]
+#' 
+.collapse_polygon = function(df) {
+
+  # WARNING: this code assumes the order of the points is correct!
+  # Connect each segment to the base (first vertex after base is number 3)
+  for (i in seq(from=3, to=nrow(df), by=2)) {
+    # Get translation in the Cartesian plane
+    diff_vector = df[(i),] - df[i-1,]
+
+    # Connect segment to the last vertex of the previous segment
+    df[(i),] = df[(i),] - diff_vector # Same as setting as df[i-1,]
+    df[(i+1),] = df[(i+1),] - diff_vector
+  }
+
+  # Remove duplicated vertices caused by connecting segments
+  df = unique(df)
+
+  return(df)
+}
+
+#' Calculates the area of the polygon.
+#' 
+#' @param df Data frame containing the coordinates in two columns: x and y
+#' 
+#' @return The area as numeric.
+#' 
+#' @seealso [polygonPlot::.collapse_polygon()]
+#' 
+#' @import checkmate
+#' @importFrom pracma polyarea
+.get_area = function(df) {
+  checkmate::assertDataFrame(x=df, col.names="named", ncols=2)
+
+  df = .collapse_polygon(df)
+
+  return(pracma::polyarea(x=df$x, y=df$y))
+}