reduced building time

vignettes/WeightedTreemaps.R

@@ -15,74 +15,74 @@ library(WeightedTreemaps)
 data(mtcars)
 mtcars$car_name = gsub(" ", "\n", row.names(mtcars))
 
-## -----------------------------------------------------------------------------
-# generate treemap; set seed to obtain same pattern every time
-tm <- voronoiTreemap(
-  data = mtcars,
-  levels = c("gear", "car_name"),
-  cell_size = "wt",
-  shape = "rounded_rect",
-  seed = 123
-)
-
-## ----fig.width = 5, fig.height = 5, out.width = "50%", fig.align = 'center'----
-drawTreemap(tm, label_size = 2.5, label_color = "white")
-
-## ----fig.width = 9, fig.height = 9, out.width = "100%", fig.align = 'center', warning = FALSE----
-drawTreemap(tm, title = "treemap 1", label_size = 2,
-  color_type = "categorical", color_level = 1,
-  layout = c(2, 2), position = c(1, 1), legend = TRUE)
-
-drawTreemap(tm, title = "treemap 2", label_size = 2,
-  color_type = "categorical", color_level = 2, border_size = 3,
-  add = TRUE, layout = c(2, 2), position = c(1, 2), legend = TRUE)
-
-drawTreemap(tm, title = "treemap 3", label_size = 2,
-  color_type = "both", color_level = 1,
-  add = TRUE, layout = c(2, 2), position = c(2, 1), legend = TRUE)
-
-drawTreemap(tm, title = "treemap 4", label_size = 2,
-  color_type = "cell_size", color_level = 2,
-  color_palette = heat.colors(10),
-  border_color = grey(0.4), label_color = grey(0.4),
-  add = TRUE, layout = c(2, 2), position = c(2, 2),
-  title_color = "black", legend = TRUE)
-
-## ----message = FALSE, error = FALSE, results = 'hide'-------------------------
-# set seed to obtain same df every time
-set.seed(123)
-df <- data.frame(A = sample(10:100, 45))
-
-tm1 <- voronoiTreemap(
-  data = df, levels = "A",
-  cell_size = "A",
-  shape = "rounded_rect",
-  positioning = "random"
-)
-
-tm2 <- voronoiTreemap(
-  data = df, levels = "A",
-  cell_size = "A",
-  shape = "rounded_rect",
-  positioning = "regular"
-)
-
-tm3 <- voronoiTreemap(
-  data = df, levels = "A",
-  cell_size = "A",
-  shape = "rounded_rect",
-  positioning = "clustered"
-)
-
-## ----fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE----
-drawTreemap(tm1, title = "positioning = 'random'", border_size = 3,
-  layout = c(1,3), position = c(1, 1))
-
-drawTreemap(tm2, title = "positioning = 'regular'", border_size = 3,
-  add = TRUE, layout = c(1,3), position = c(1, 2))
-
-drawTreemap(tm3, title = "positioning = 'clustered'", border_size = 3,
-  add = TRUE, layout = c(1,3), position = c(1, 3))
+## ----eval = FALSE-------------------------------------------------------------
+#  # generate treemap; set seed to obtain same pattern every time
+#  tm <- voronoiTreemap(
+#    data = mtcars,
+#    levels = c("gear", "car_name"),
+#    cell_size = "wt",
+#    shape = "rounded_rect",
+#    seed = 123
+#  )
+
+## ----fig.width = 5, fig.height = 5, out.width = "50%", fig.align = 'center', eval = FALSE----
+#  drawTreemap(tm, label_size = 2.5, label_color = "white")
+
+## ----fig.width = 9, fig.height = 9, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE----
+#  drawTreemap(tm, title = "treemap 1", label_size = 2,
+#    color_type = "categorical", color_level = 1,
+#    layout = c(2, 2), position = c(1, 1), legend = TRUE)
+#  
+#  drawTreemap(tm, title = "treemap 2", label_size = 2,
+#    color_type = "categorical", color_level = 2, border_size = 3,
+#    add = TRUE, layout = c(2, 2), position = c(1, 2), legend = TRUE)
+#  
+#  drawTreemap(tm, title = "treemap 3", label_size = 2,
+#    color_type = "both", color_level = 1,
+#    add = TRUE, layout = c(2, 2), position = c(2, 1), legend = TRUE)
+#  
+#  drawTreemap(tm, title = "treemap 4", label_size = 2,
+#    color_type = "cell_size", color_level = 2,
+#    color_palette = heat.colors(10),
+#    border_color = grey(0.4), label_color = grey(0.4),
+#    add = TRUE, layout = c(2, 2), position = c(2, 2),
+#    title_color = "black", legend = TRUE)
+
+## ----message = FALSE, error = FALSE, results = 'hide', eval = FALSE-----------
+#  # set seed to obtain same df every time
+#  set.seed(123)
+#  df <- data.frame(A = sample(10:100, 45))
+#  
+#  tm1 <- voronoiTreemap(
+#    data = df, levels = "A",
+#    cell_size = "A",
+#    shape = "rounded_rect",
+#    positioning = "random"
+#  )
+#  
+#  tm2 <- voronoiTreemap(
+#    data = df, levels = "A",
+#    cell_size = "A",
+#    shape = "rounded_rect",
+#    positioning = "regular"
+#  )
+#  
+#  tm3 <- voronoiTreemap(
+#    data = df, levels = "A",
+#    cell_size = "A",
+#    shape = "rounded_rect",
+#    positioning = "clustered"
+#  )
+
+## ----fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE----
+#  drawTreemap(tm1, title = "positioning = 'random'", border_size = 3,
+#    layout = c(1,3), position = c(1, 1))
+#  
+#  drawTreemap(tm2, title = "positioning = 'regular'", border_size = 3,
+#    add = TRUE, layout = c(1,3), position = c(1, 2))
+#  
+#  drawTreemap(tm3, title = "positioning = 'clustered'", border_size = 3,
+#    add = TRUE, layout = c(1,3), position = c(1, 3))
 
 ## -----------------------------------------------------------------------------
 # different initial shapes, the more squared the better
@@ -99,20 +99,20 @@ oct_coord <- list(
   y = cos(seq(0, 2, 2/8)*pi) * 1000 + 1000
 )
 
-## ----message = FALSE, error = FALSE, results = 'hide'-------------------------
-tm1 <- voronoiTreemap(data = df, levels = "A",
-  shape = house_coords)
-
-tm2 <- voronoiTreemap(data = df, levels = "A",
-  shape = rect_coords)
-
-tm3 <- voronoiTreemap(data = df, levels = "A",
-  shape = oct_coord)
-
-## ----fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE----
-drawTreemap(tm1, layout = c(1,3), position = c(1, 1))
-drawTreemap(tm2, add = TRUE, layout = c(1,3), position = c(1, 2))
-drawTreemap(tm3, add = TRUE, layout = c(1,3), position = c(1, 3))
+## ----message = FALSE, error = FALSE, results = 'hide', eval = FALSE-----------
+#  tm1 <- voronoiTreemap(data = df, levels = "A",
+#    shape = house_coords)
+#  
+#  tm2 <- voronoiTreemap(data = df, levels = "A",
+#    shape = rect_coords)
+#  
+#  tm3 <- voronoiTreemap(data = df, levels = "A",
+#    shape = oct_coord)
+
+## ----fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE----
+#  drawTreemap(tm1, layout = c(1,3), position = c(1, 1))
+#  drawTreemap(tm2, add = TRUE, layout = c(1,3), position = c(1, 2))
+#  drawTreemap(tm3, add = TRUE, layout = c(1,3), position = c(1, 3))
 
 ## -----------------------------------------------------------------------------
 # generate data frame

vignettes/WeightedTreemaps.Rmd

@@ -1,7 +1,7 @@
 ---
 output:  rmarkdown::html_vignette
 title: "WeightedTreemaps"
-author: "Michael Jahn, David Leslie, Ahmadou Dicko"
+author: "Michael Jahn, David Leslie, Ahmadou Dicko, Paul Murrell"
 date: "`r Sys.Date()`"
 vignette: >
   %\VignetteIndexEntry{WeightedTreemaps}
@@ -65,7 +65,7 @@ Generate the treemap. It will return a list of polygons and metadata.
 The columns of the data frame that are used as levels of the treemap need to be specified.
 Different parameters like the initial shape, or the maximum number of iterations are optional.
 
-```{r}
+```{r, eval = FALSE}
 # generate treemap; set seed to obtain same pattern every time
 tm <- voronoiTreemap(
   data = mtcars,
@@ -78,14 +78,15 @@ tm <- voronoiTreemap(
 
 Draw the treemap.
 
-```{r, fig.width = 5, fig.height = 5, out.width = "50%", fig.align = 'center'}
+```{r, fig.width = 5, fig.height = 5, out.width = "50%", fig.align = 'center', eval = FALSE}
 drawTreemap(tm, label_size = 2.5, label_color = "white")
 ```
 
+<img src="png/unnamed-chunk-4-1.png" align="center" width="50%" />
 
 The `voronoiTreemap()` and `drawTreemap()` functions are separated in order to allow drawing of the same treemap object in different ways. Computation of treemaps with thousands of cells can be very time and resource consuming (around 5-10 minutes for a 2000-cell treemap on a regular desktop computer). With the `drawTreemap()` function, we can not only plot the same treemap in different ways but also combine several treemaps on one page using the `layout` and `position` arguments. The most important style element is color. Coloring can be based on cell category, cell size, or both, using the `color_type` argument. By default, the highest hierarchical level is used for coloring but that can be customized using the `color_level` argument.
 
-```{r, fig.width = 9, fig.height = 9, out.width = "100%", fig.align = 'center', warning = FALSE}
+```{r, fig.width = 9, fig.height = 9, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE}
 drawTreemap(tm, title = "treemap 1", label_size = 2,
   color_type = "categorical", color_level = 1,
   layout = c(2, 2), position = c(1, 1), legend = TRUE)
@@ -106,12 +107,13 @@ drawTreemap(tm, title = "treemap 4", label_size = 2,
   title_color = "black", legend = TRUE)
 ```
 
+<img src="png/unnamed-chunk-5-1.png" align="center" width="100%" />
 
 ### Positioning of cells
 
 Generating a Voronoi treemap is an iterative and somewhat random process. Since the cells 'move' during the iteration process, it can be difficult to control the exact final position of cells. However, there are two ways to influence cell positioning. The first is to use different algorithms for sampling initial coordinates for each cell. The second is simply setting a seed, which will sample the same set of starting coordinates for the same input data. Regarding the `positioning` argument, compare the following three examples where initial positions are 1) random, 2) ordered from top to bottom, or 3) ordered from center to edges.
 
-```{r, message = FALSE, error = FALSE, results = 'hide'}
+```{r, message = FALSE, error = FALSE, results = 'hide', eval = FALSE}
 # set seed to obtain same df every time
 set.seed(123)
 df <- data.frame(A = sample(10:100, 45))
@@ -139,7 +141,7 @@ tm3 <- voronoiTreemap(
 ```
 
 
-```{r, fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE}
+```{r, fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE}
 drawTreemap(tm1, title = "positioning = 'random'", border_size = 3,
   layout = c(1,3), position = c(1, 1))
 
@@ -150,6 +152,8 @@ drawTreemap(tm3, title = "positioning = 'clustered'", border_size = 3,
   add = TRUE, layout = c(1,3), position = c(1, 3))
 ```
 
+<img src="png/unnamed-chunk-7-1.png" align="center" width="100%" />
+
 ### Custom initial shapes
 
 Instead of using predefined shapes, we can also supply a custom set of coordinates to plot a treemap using the `shape` argument. The validity of the supplied coordinates is not checked, so all responsibility lies with the user (!). The R session might even crash (due to C++ dependency) if a shape is supplied that is too irregular or edgy, and the tesselation becomes unfeasible. Here are some stable examples.
@@ -172,7 +176,7 @@ oct_coord <- list(
 
 Let's generate treemaps with the shapes of a house, a wide rectangle, and an octogon.
 
-```{r, message = FALSE, error = FALSE, results = 'hide'}
+```{r, message = FALSE, error = FALSE, results = 'hide', eval = FALSE}
 tm1 <- voronoiTreemap(data = df, levels = "A",
   shape = house_coords)
 
@@ -184,12 +188,14 @@ tm3 <- voronoiTreemap(data = df, levels = "A",
 ```
 
 
-```{r, fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE}
+```{r, fig.width = 12, fig.height = 4, out.width = "100%", fig.align = 'center', warning = FALSE, eval = FALSE}
 drawTreemap(tm1, layout = c(1,3), position = c(1, 1))
 drawTreemap(tm2, add = TRUE, layout = c(1,3), position = c(1, 2))
 drawTreemap(tm3, add = TRUE, layout = c(1,3), position = c(1, 3))
 ```
 
+<img src="png/unnamed-chunk-10-1.png" align="center" width="100%" />
+
 ### Sunburst treemaps
 
 Sunburst treemaps are generated in the same way as described above for Voronoi treemaps.