update website

.Rbuildignore

@@ -12,3 +12,15 @@ revdep/
 ^docs$
 ^pkgdown$
 build_pkg_site.R
+
+vignettes/annotate.Rmd
+vignettes/examples.Rmd
+vignettes/jquery.min.js
+vignettes/jquery.sticky.js
+vignettes/main.css
+vignettes/qing_ming_shang_he_tu.png
+vignettes/qing_ming_shang_he_tu_small.png
+vignettes/special_data_type.Rmd
+vignettes/spiralize_git_commit.Rmd
+vignettes/spiralize_intro.Rmd
+vignettes/tree_of_life.Rmd

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: spiralize
 Type: Package
 Title: Visualize Data on Spirals
-Version: 1.0.8
-Date: 2023-12-02
+Version: 1.0.9
+Date: 2024-02-26
 Authors@R: person("Zuguang", "Gu", email = "[email protected]", role = c("aut", "cre"),
                   comment = c('ORCID'="0000-0002-7395-8709"))
-Depends: R (>= 3.6.0), grid
+Depends: R (>= 4.0.0), grid
 Imports: GlobalOptions (>= 0.1.1), 
          GetoptLong (>= 0.1.8), 
          circlize,
@@ -28,10 +28,14 @@ Suggests: ComplexHeatmap,
           dendextend,
           bezier,
           magick
-Description: It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart. 
+Description: It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, 
+    makes so-called spiral graph or spiral chart. 
     It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high 
     resolution. 2. It is efficient for time series data to reveal periodic patterns.
 VignetteBuilder: knitr
-URL: https://github.com/jokergoo/spiralize
+URL: https://github.com/jokergoo/spiralize, https://jokergoo.github.io/spiralize
 License: MIT + file LICENSE
 NeedsCompilation: no
+RoxygenNote: 7.2.3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)

LICENSE

@@ -1,3 +1,21 @@
-YEAR: 2021
+YEAR: 2024
 COPYRIGHT HOLDER: Zuguang Gu
 
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

R/git_commits.R

@@ -17,7 +17,8 @@ spiral_git_commits = function(repo = ".", show_legend = TRUE,
     start = NULL, end = Sys.Date(),
     pt_range = c(2, 16), commits_range = c(2, 20),
     type = c("points", "heatmap"),
-    colors = c("#3288BD", "#99D594", "#E6F598", "#FFFFBF", "#FEE08B", "#FC8D59", "#D53E4F")) {
+    colors = c("#3288BD", "#99D594", "#E6F598", "#FFFFBF", 
+               "#FEE08B", "#FC8D59", "#D53E4F")) {
 
     type = match.arg(type)[1]
 

R/transform.R

@@ -339,7 +339,7 @@ flip_theta_back = function(theta) {
 #
 # == details
 # The data points are assigned to the nearest inner loops. Denote the a data point has a coordinate (r, theta)
-# in the polar coordinate system, r_k and r_{k+1} are the radius of the two loops at theta + 2*pi*a and theta + 2*pi*(a+1) that below and above the data point,
+# in the polar coordinate system, r_k and r_(k+1) are the radius of the two loops at theta + 2*pi*a and theta + 2*pi*(a+1) that below and above the data point,
 # the data point is assigned to the loop k.
 #
 # == value

README.md

@@ -78,37 +78,24 @@ Spiral plot can also visualize dendrograms with large number of leaves, thus the
 - `spiral_phylo()` 
 
 
-## Vignettes
-
-There are the following vignettes:
-
-- [Visualize Data on Spirals](https://jokergoo.github.io/spiralize_vignettes/spiralize.html). It gives an detailed introduction of the _spiralize_ package.
-- [Initialize Spirals by Special Data Types](https://jokergoo.github.io/spiralize_vignettes/special_data_type.html). It introduces how to specifically create spiral plot with time series data and genomic data.
-- [Annotate the Plot](https://jokergoo.github.io/spiralize_vignettes/annotate.html). It introduces how to add annotations and how to add legends to the plot.
-- [Real World Examples](https://jokergoo.github.io/spiralize_vignettes/examples.html). It contains many examples with real world datasets.
-- [Visualize tree of life of 50455 species](https://jokergoo.github.io/spiralize_vignettes/tree_of_life.html).
-
-
 ## Examples
 
 1. Difference of **ggplot2** daily downloads to the mean of the current year (2015-2021). Each loop contains 52 weeks so that same weeks in different years locate at the same angle in the polar coordinates.
 
-![image](https://user-images.githubusercontent.com/449218/122206336-8c125400-cea1-11eb-8b0d-2314aede4641.png)
+![](https://user-images.githubusercontent.com/449218/122206336-8c125400-cea1-11eb-8b0d-2314aede4641.png)
 
 2. The same data as the first one, but horizon chart is used. Also title and legends are added.
 
-![image](https://user-images.githubusercontent.com/449218/122206221-671de100-cea1-11eb-823e-6c48de851667.png)
+![](https://user-images.githubusercontent.com/449218/122206221-671de100-cea1-11eb-823e-6c48de851667.png)
 
 
 3. A phylogenetic life tree with 50645 species. 
 
-![download](https://user-images.githubusercontent.com/449218/123804978-fbe6fc80-d8ed-11eb-93d8-d3f83d552dde.png)
+![](https://user-images.githubusercontent.com/449218/123804978-fbe6fc80-d8ed-11eb-93d8-d3f83d552dde.png)
 
 4. The spiral COVID-19 Shiny app
 
-https://jokergoooo.shinyapps.io/covid19/
-
-![covid19_spiral](https://user-images.githubusercontent.com/449218/154753102-d66b3588-eca1-471b-bdfe-2c147ed257f5.gif)
+![](https://user-images.githubusercontent.com/449218/154753102-d66b3588-eca1-471b-bdfe-2c147ed257f5.gif)
 
 
 ## License

_pkgdown.yml

@@ -1 +1,28 @@
 destination: docs
+
+navbar:
+  title: "spiralize"
+  left:
+    - text: "Articles"
+      menu:
+        - text: Vignettes
+        - text: "Visualize Data on Spirals"
+          href: articles/spiralize_intro.html
+        - text: "Initialize Spirals by Special Data Types"
+          href: articles/special_data_type.html
+        - text: "Annotate the Plot"
+          href: articles/annotate.html
+        - text: "Real World Examples"
+          href: articles/examples.html
+        - text: "Visualize tree of life"
+          href: articles/tree_of_life.html
+        - text: -------
+        - text: More applications
+        - text: "Spiral visualization on git commits of a git repo"
+          href: articles/spiralize_git_commit.html
+    - text: "Reference"
+      href: reference/index.html
+
+template:
+  includes:
+    after_body: "<style>nav[data-toggle='toc'] .nav .nav {display: block;}</style>"

build_pkg_site.R

@@ -1,4 +1,3 @@
-writeLines("destination: docs", "_pkgdown.yml")
 if(file.exists(".Rbuildignore")) {
 	ln = readLines(".Rbuildignore")
 	if(!any(ln == "^_pkgdown\\.yml$")) {
@@ -20,5 +19,21 @@ if(file.exists(".Rbuildignore")) {
 ^docs$
 ^pkgdown$", ".Rbuildignore")
 }
+
+pkgname = read.dcf("DESCRIPTION")[1, "Package"]
+
+vig_files = list.files(path = "vignettes", full.names = TRUE)
+vig_files = vig_files[basename(vig_files) != paste0(pkgname, ".Rmd")]
+
+ln = readLines(".Rbuildignore")
+
+for(v in vig_files) {
+	if(!any(ln == v)) {
+		ln = c(ln, v)
+	}
+}
+writeLines(ln, ".Rbuildignore")
+
+
 options(rmarkdown.html_vignette.check_title = FALSE)
 pkgdown::build_site(run_dont_run = TRUE)