Merge pull request #61 from dusadrian/master

Meet copyright regulation of venn

DESCRIPTION

@@ -7,7 +7,7 @@ Authors@R: c(
   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("ctb"), comment = c(ORCID = "0000-0002-6485-8781")),
   person("Adrian", "Dusa",  email = "dusa.adrian@unibuc.ro", role = c("aut","cph"), 
     comment = c(ORCID = "0000-0002-3525-9253", 
-    note = "Adrian Dusa is the author and copyright holder of venn, where ggVennDiagram import polygon coordinates to enabling 5 - 7 sets Venn diagram.")),
+    note = "Adrian Dusa is the author and copyright holder of venn, where ggVennDiagram imports the polygon coordinates enabling 5 - 7 sets Venn diagram.")),
   person("Turgut Yigit", "Akyol", email = "tyakyol@gmail.com", role = c("ctb"), comment=c(ORCID = "0000-0003-0897-7716"))
   )
 Maintainer: Chun-Hui Gao <gaospecial@gmail.com>
@@ -28,7 +28,7 @@ Imports:
     methods,
     tibble,
     aplot,
-    venn (>= 1.11),
+    venn (>= 1.12),
     yulab.utils,
     forcats
 URL: https://github.com/gaospecial/ggVennDiagram, https://gaospecial.github.io/ggVennDiagram/

README.rmd

@@ -148,7 +148,7 @@ The key point is to let the generated ellipses have exactly one intersection for
 
 ## Venn Diagram of up to seven sets
 
-From v1.0, `ggVennDiagram` can plot up to seven dimension Venn plot. Please note that the shapes for this five sets diagram, as well as those for six and seven sets, are imported from the original package “venn”, authored by Adrian Dușa.
+From v1.0, `ggVennDiagram` can plot up to seven dimension Venn plot. Please note that the shapes for this five sets diagram, as well as those for six and seven sets, are imported from the original package [`venn`](https://CRAN.R-project.org/package=venn) authored by Adrian Dușa.
 
 However, Venn Diagram for more than four sets may be meaningless in some conditions, 
 as some parts may be omitted in such ellipses. Therefore, it is only useful in specific conditions. 

less-dependency.Rmd

@@ -37,7 +37,7 @@ x <- list(A=sample(genes,300),
 
 ```{r}
 dependency = c(
-     "sf",
+    "sf",
     "ggplot2",
     "dplyr",
     "stringr",
@@ -68,9 +68,9 @@ deps |> select(package, filesize) |>
 Among them, `sf` is the heaviest package that `ggVennDiagram` depend on. 
 
 ```{r}
-pak_dep = deps %>%
-  select(package, sysreqs, filesize) %>%
-  arrange(desc(filesize)) %>%
+pak_dep = deps |>
+  select(package, sysreqs, filesize) |>
+  arrange(desc(filesize)) |>
   filter(package %in% dependency)
 pak_dep
 ```
@@ -82,11 +82,11 @@ pak_dep |>
 ```
 
 
-`sf` not only have the largest size of package, but also depends on several system packages, such as `GDAL`, `GEOS`, `PROJ`, and so on. Furthermore, two of the `sf`-dependent packages, `s2` and `units` also have system requirements, especially `units`, whose system dependence `udunits-2` is an additional one that usually not installed by most of the `ggVennDiagram` users.
+Package `sf` not only has the largest size, but also depends on several system packages, such as `GDAL`, `GEOS`, `PROJ`, and so on. Furthermore, two of the `sf`-dependent packages, `s2` and `units` also have system requirements, especially `units`, whose system dependence `udunits-2` is an additional one that usually not installed by most of the `ggVennDiagram` users.
 
 ```{r}
 deps_sf = pak::pkg_deps("sf")
-deps %>% filter(package %in% deps_sf$package, sysreqs != "") %>% 
+deps |> filter(package %in% deps_sf$package, sysreqs != "") |> 
   select(package, sysreqs, filesize)
 ```
 
@@ -97,10 +97,10 @@ However, `sf` is a necessary for the full functions of `ggVennDiagram` in shape
 Besides, several other packages are removed from dependency list after considerations.
 
 ```{r}
-deps %>%
-  select(package, sysreqs, filesize) %>%
+deps |>
+  select(package, sysreqs, filesize) |>
   filter(!package %in% pak::pkg_deps("sf")$package, 
-         !package %in% pak::pkg_deps("ggplot2")$package) %>% 
+         !package %in% pak::pkg_deps("ggplot2")$package) |> 
   arrange(desc(filesize))
 ```
 
@@ -127,14 +127,15 @@ dependency_new = c(
   "methods",
   "tibble",
   "aplot",
-  "forcats")
+  "forcats",
+  "venn")
 ```
 
 
 ```{r}
-primary_deps = deps_new %>%
-  select(package, sysreqs, filesize) %>%
-  arrange(desc(filesize)) %>%
+primary_deps = deps_new |>
+  select(package, sysreqs, filesize) |>
+  arrange(desc(filesize)) |>
   filter(package %in% dependency_new)
 primary_deps
 # write.csv(primary_deps, file = "deps_current.csv")

vignettes/.gitignore

@@ -1,2 +1,3 @@
 *.html
 *.R
+ggVennDiagram.Rproj

vignettes/using-new-shapes.Rmd

@@ -50,14 +50,14 @@ shape2 = get_shape_by_id("401f")
 plot_shape_edge(shape2)
 ```
 
-The `plot_shapes()` function can be used to plot all the available shapes stored in this package. Please note that the shapes for this five sets diagram, as well as those for six and seven sets, are imported from the original package “venn”, authored by Adrian Dușa.
+The `plot_shapes()` function can be used to plot all the available shapes stored in this package. Please note that the shapes for this five sets diagram, as well as those for six and seven sets, are imported from the original package [`venn`](https://CRAN.R-project.org/package=venn), authored by Adrian Dușa.
 
 
 ```{r}
 plot_shapes()
 ```
 
-Among them, the shapes with less than four sets can be generated with circle or ellipses. For example, the parameters used to generate four-set ellipses were adopted from `VennDiagram` (<https://CRAN.R-project.org/package=VennDiagram>). Notably, those shapes of five or more sets, including 501, 502, 601, and 701, are collected by Adrian Dusa and provided in his `venn` package (<https://CRAN.R-project.org/package=venn>). Besides, the 601t shape is imported from a WiKi entry (<https://en.wikipedia.org/wiki/Venn_diagram>).
+Among them, the shapes with less than four sets can be generated with circle or ellipses. For example, the parameters used to generate four-set ellipses were adopted from `VennDiagram` (<https://CRAN.R-project.org/package=VennDiagram>). Notably, those shapes of five or more sets, including 501, 502, 601, and 701, are created by Adrian Dușa and provided in his `venn` package (<https://CRAN.R-project.org/package=venn>). Besides, the 601t shape is imported from a WiKi entry (<https://en.wikipedia.org/wiki/Venn_diagram>).
 
 
 ## Using alternative internal shapes