fix: cran warnings

bench.R

@@ -0,0 +1,149 @@
+library(tidyverse)
+library(UpSetR)
+library(upsetjs)
+
+# loading example files
+toyset_1 <- read_delim(
+  file = gzfile("./r_package/tests/testthat/data/toyset_1.tsv.gz"),
+  delim = "\t",
+  escape_double = FALSE,
+  trim_ws = TRUE
+) %>%
+  data.frame()
+
+toyset_2 <- read_delim(
+  file = gzfile("./r_package/tests/testthat/data/toyset_2.tsv.gz"),
+  delim = "\t",
+  escape_double = FALSE,
+  trim_ws = TRUE
+) %>%
+  data.frame()
+
+# for upsetR aesthetics
+count <- toyset_1 %>%
+  group_by(attribute1) %>%
+  count() %>%
+  arrange(attribute1)
+
+# upsetR version of toyset_1
+## basic
+start <- Sys.time()
+upset(
+  data = toyset_1,
+  sets = c(
+    "toy1",
+    "toy2",
+    "toy3",
+    "toy4",
+    "toy5",
+    "toy6"
+  ),
+  order.by = "freq",
+  set_size.show = TRUE,
+  set_size.scale_max = 20000,
+)
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+## advanced (would be really nice to have such coloring options)
+start <- Sys.time()
+upset(
+  data = toyset_1,
+  sets = c(
+    "toy1",
+    "toy2",
+    "toy3",
+    "toy4",
+    "toy5",
+    "toy6"
+  ),
+  query.legend = "top",
+  queries = list(
+    list(
+      query = elements,
+      params = list(
+        "attribute1",
+        c(
+          count[1, 1],
+          count[2, 1],
+          count[3, 1]
+        )
+      ),
+      active = TRUE,
+      color = "#b2df8a",
+      query.name = "kin"
+    ),
+    list(
+      query = elements,
+      params = list(
+        "attribute1",
+        c(
+          count[3, 1],
+          count[2, 1]
+        )
+      ),
+      active = TRUE,
+      color = "#1f78b4",
+      query.name = "ord"
+    ),
+    list(
+      query = elements,
+      params = list(
+        "attribute1",
+        c(count[3, 1])
+      ),
+      active = TRUE,
+      color = "#a6cee3",
+      query.name = "spe"
+    )
+  ),
+  order.by = "freq",
+  set_size.show = TRUE,
+  set_size.scale_max = 20000
+)
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+## bigger matrix () 209'301 x 33 (still not that big imho)
+start <- Sys.time()
+upset(
+  toyset_2,
+  order.by = "freq",
+  set_size.show = TRUE,
+  set_size.scale_max = 250000
+)
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+# upsetjs version of toyset_1
+## works nicely
+start <- Sys.time()
+upsetjs() %>%
+  fromDataFrame(toyset_1[,1:6], c_type="distinctIntersection") %>%
+  interactiveChart()
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+start <- Sys.time()
+upset(
+ toyset_2,
+   order.by = "freq",
+   set_size.show = TRUE,
+   set_size.scale_max = 250000,
+   nsets = 33
+)
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+# upsetjs version of toyset_2
+## last for ages, no idea why... never had the patience to wait until the end
+start <- Sys.time()
+
+upsetjs() %>%
+  fromDataFrame(toyset_2, c_type="distinctIntersection", store.elems=FALSE, limit = 40) %>%
+  interactiveChart()
+
+end <- Sys.time()
+cat("Plotted  in", format(end - start), "\n")
+
+# Thanks a lot

r_package/R/data.R

@@ -286,7 +286,9 @@ extractSetsFromDataFrame = function(df,
 #' @param shared.mode whether on 'hover' or 'click' (default) is synced
 #' @param colors the optional list with set name to color
 #' @param c_type the combination type to use
+#' @param store.elems whether to store the set elements within the structures (set to false for big data frames)
 #' @return the object given as first argument
+#' @importFrom stats aggregate
 #' @examples
 #' df <- as.data.frame(list(a=c(1, 1, 1),b=c(0, 1, 1)),row.names=c('a', 'b', 'c'))
 #' upsetjs() %>% fromDataFrame(df)