update the website

.Rbuildignore

@@ -24,3 +24,9 @@ vignettes/special_data_type.Rmd
 vignettes/spiralize_git_commit.Rmd
 vignettes/spiralize_intro.Rmd
 vignettes/tree_of_life.Rmd
+vignettes/git_commit_julia.png
+vignettes/git_commit_perl.png
+vignettes/git_commit_python.png
+vignettes/git_commit_r.png
+vignettes/more_examples.Rmd
+vignettes/spiral_covid.Rmd

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: spiralize
 Type: Package
 Title: Visualize Data on Spirals
-Version: 1.0.9
-Date: 2024-02-26
+Version: 1.1.0
+Date: 2024-06-11
 Authors@R: person("Zuguang", "Gu", email = "[email protected]", role = c("aut", "cre"),
                   comment = c('ORCID'="0000-0002-7395-8709"))
 Depends: R (>= 4.0.0), grid
@@ -22,12 +22,12 @@ Suggests: ComplexHeatmap,
           jpeg,
           png,
           tiff,
-          ape,
           cranlogs,
           cowplot,
           dendextend,
           bezier,
-          magick
+          magick,
+          ape
 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 
@@ -36,6 +36,6 @@ VignetteBuilder: knitr
 URL: https://github.com/jokergoo/spiralize, https://jokergoo.github.io/spiralize
 License: MIT + file LICENSE
 NeedsCompilation: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

LICENSE

@@ -1,21 +1,2 @@
 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.
-

NAMESPACE

@@ -1,59 +1,69 @@
-S3method("$", "TRACK_META")
-export("$.TRACK_META")
-S3method("names", "TRACK_META")
-export("names.TRACK_META")
-S3method("print", "TRACK_META")
-export("print.TRACK_META")
-export("TRACK_META")
-export("cartesian_to_xy")
-export("current_spiral")
-export("current_spiral_vp")
-export("current_track_index")
-export("get_track_data")
-export("horizon_legend")
-export("is_in_track")
-export("n_tracks")
-export("phylo_to_dendrogram")
-export("polar_to_cartesian")
-export("set_current_track")
-export("solve_theta_from_spiral_length")
-export("spiral_arrow")
-export("spiral_axis")
-export("spiral_bars")
-export("spiral_clear")
-export("spiral_dendrogram")
-export("spiral_git_commits")
-export("spiral_highlight")
-export("spiral_highlight_by_sector")
-export("spiral_horizon")
-export("spiral_info")
-export("spiral_initialize")
-export("spiral_initialize_by_gcoor")
-export("spiral_initialize_by_time")
-export("spiral_lines")
-export("spiral_opt")
-export("spiral_phylo")
-export("spiral_points")
-export("spiral_polygon")
-export("spiral_raster")
-export("spiral_rect")
-export("spiral_segments")
-export("spiral_text")
-export("spiral_track")
-export("spiral_xaxis")
-export("spiral_yaxis")
-export("xy_to_cartesian")
-export("xy_to_polar")
+# Generated by roxygen2: do not edit by hand
 
-import("GlobalOptions")
-import(GetoptLong)
+S3method("$",TRACK_META)
+S3method("[",TRACK_META)
+S3method("[[",TRACK_META)
+S3method(names,TRACK_META)
+S3method(print,TRACK_META)
+export(TRACK_META)
+export(cartesian_to_polar)
+export(cartesian_to_xy)
+export(current_spiral)
+export(current_spiral_vp)
+export(current_track_index)
+export(get_track_data)
+export(horizon_legend)
+export(is_in_track)
+export(n_tracks)
+export(phylo_to_dendrogram)
+export(polar_to_cartesian)
+export(set_current_track)
+export(solve_theta_from_spiral_length)
+export(spiral_arrow)
+export(spiral_axis)
+export(spiral_bars)
+export(spiral_clear)
+export(spiral_dendrogram)
+export(spiral_git_commits)
+export(spiral_highlight)
+export(spiral_highlight_by_sector)
+export(spiral_horizon)
+export(spiral_info)
+export(spiral_initialize)
+export(spiral_initialize_by_gcoor)
+export(spiral_initialize_by_time)
+export(spiral_lines)
+export(spiral_opt)
+export(spiral_phylo)
+export(spiral_pkg_downloads)
+export(spiral_points)
+export(spiral_polygon)
+export(spiral_raster)
+export(spiral_rect)
+export(spiral_segments)
+export(spiral_text)
+export(spiral_track)
+export(spiral_xaxis)
+export(spiral_yaxis)
+export(xy_to_cartesian)
+export(xy_to_polar)
+import(GlobalOptions)
 import(grid)
 import(lubridate)
 import(methods)
-importFrom("circlize", colorRamp2, rand_color)
-importFrom("grDevices", "as.raster", "png", "dev.off")
-importFrom("grDevices", "col2rgb", "rgb", "dev.size", "pdf.options")
-importFrom("utils", "getFromNamespace", "packageDescription")
-importFrom("utils", "read.table")
-importFrom(stats, is.leaf, uniroot)
-
+importFrom(GetoptLong,qq)
+importFrom(GetoptLong,qqcat)
+importFrom(circlize,colorRamp2)
+importFrom(circlize,rand_color)
+importFrom(grDevices,as.raster)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,dev.size)
+importFrom(grDevices,pdf.options)
+importFrom(grDevices,png)
+importFrom(grDevices,rgb)
+importFrom(stats,is.leaf)
+importFrom(stats,quantile)
+importFrom(stats,uniroot)
+importFrom(utils,getFromNamespace)
+importFrom(utils,read.table)

NEWS

@@ -1,3 +1,8 @@
+## version 1.1.0
+
+- use roxygen2 to generate documentations
+- redesigned the website
+
 ## version 1.0.8
 
 - add `spiral_git_commits()`.

R/dendrogram.R

@@ -1,3 +1,5 @@
+
+#' @importFrom stats is.leaf
 construct_dend_segments = function(dend, gp = gpar()) {
 
     if(!requireNamespace("ComplexHeatmap")) {
@@ -113,32 +115,34 @@ construct_dend_segments = function(dend, gp = gpar()) {
 
 }
 
-# == title
-# Draw dendrogram
-#
-# == param
-# -dend A ``stats::dendrogram`` object.
-# -gp Graphics parameters of the dendrogram edges.
-# -track_index Index of the track. 
-#
-# == details
-# Note the dendrogram edges can be rendered with the `dendextend::dendextend` package.
-#
-# == value
-# Height of the dendrogram.
-#
-# == example
-# k = 500
-# dend = as.dendrogram(hclust(dist(runif(k))))
-# spiral_initialize(xlim = c(0, k), start = 360, end = 360*3)
-# spiral_track(height = 0.8, background_gp = gpar(fill = "#EEEEEE", col = NA))
-#
-# \donttest{
-# require(dendextend)
-# dend = color_branches(dend, k = 4)
-# spiral_initialize(xlim = c(0, k), start = 360, end = 360*3)
-# spiral_track(height = 0.8, background_gp = gpar(fill = "#EEEEEE", col = NA))
-# }
+#' Draw dendrogram
+#'
+#' @param dend A [`stats::dendrogram`] object.
+#' @param gp Graphical parameters of the dendrogram edges, mainly as a global setting.
+#' @param track_index Index of the track. 
+#'
+#' @details
+#' Graphical parameters for individual edges can be set via the `edgePar` attribute on each node in the dendrogram, see [`stats::dendrogram`]
+#' for how to set `edgePar`.
+#' 
+#' The dendrogram edges can also be rendered by [`dendextend::color_branches()`].
+#'
+#' @return Height of the dendrogram.
+#' @export
+#' @examples
+#' k = 500
+#' dend = as.dendrogram(hclust(dist(runif(k))))
+#' spiral_initialize(xlim = c(0, k), start = 360, end = 360*3)
+#' spiral_track(height = 0.8, background_gp = gpar(fill = "#EEEEEE", col = NA))
+#' spiral_dendrogram(dend)
+#'
+#' \donttest{
+#' require(dendextend)
+#' dend = color_branches(dend, k = 4)
+#' spiral_initialize(xlim = c(0, k), start = 360, end = 360*3)
+#' spiral_track(height = 0.8, background_gp = gpar(fill = "#EEEEEE", col = NA))
+#' spiral_dendrogram(dend)
+#' }
 spiral_dendrogram = function(dend, gp = gpar(), track_index = current_track_index()) {
 
     lt = construct_dend_segments(dend, gp)
@@ -160,6 +164,7 @@ spiral_dendrogram = function(dend, gp = gpar(), track_index = current_track_inde
 
 ############# for phylo object ############
 
+#' @importFrom circlize rand_color
 construct_phylo_segments = function(obj, group = NULL, group_col = NULL) {
     if(!inherits(obj, "phylo")) {
         stop_wrap("The input should be a 'phylo' object.")
@@ -275,28 +280,25 @@ construct_phylo_segments = function(obj, group = NULL, group_col = NULL) {
 
 }
 
-# == title
-# Draw phylogenetic tree
-#
-# == param
-# -obj A ``phylo`` object.
-# -gp Graphics parameters of the tree edges.
-# -log Whether the height of the tree should be log-transformed (log10(x + 1))?
-# -reverse Whether the tree should be reversed?
-# -group A categorical variable for splitting the tree.
-# -group_col A named vector which contains group colors.
-# -track_index Index of the track. 
-#
-# == value
-# Height of the phylogenetic tree.
-#
-# == example
-# require(ape)
-# data(bird.families)
-# n = length(bird.families$tip.label)
-# spiral_initialize(xlim = c(0, n), start = 360, end = 360*3)
-# spiral_track(height = 0.8)
-# spiral_phylo(bird.families)
+#' Draw phylogenetic tree
+#'
+#' @param obj A [`stats::dendrogram`] object.
+#' @param gp Graphical parameters of the tree edges, mainly as a global setting.
+#' @param log Whether the height of the tree to be log-transformed `log10(x + 1)`?
+#' @param reverse Whether the tree to be reversed?
+#' @param group A categorical variable for splitting the tree.
+#' @param group_col A named vector which contains group colors.
+#' @param track_index Index of the track. 
+#'
+#' @return Height of the phylogenetic tree.
+#' @export
+#' @examples
+#' require(ape)
+#' data(bird.families)
+#' n = length(bird.families$tip.label)
+#' spiral_initialize(xlim = c(0, n), start = 360, end = 360*3)
+#' spiral_track(height = 0.8)
+#' spiral_phylo(bird.families)
 spiral_phylo = function(obj, gp = gpar(), log = FALSE, reverse = FALSE, 
     group = NULL, group_col = NULL, track_index = current_track_index()) {
 
@@ -333,31 +335,25 @@ spiral_phylo = function(obj, gp = gpar(), log = FALSE, reverse = FALSE,
     invisible(ymax2)
 }
 
-# == title
-# Convert a phylo object to a dendrogram object
-#
-# == param
-# -obj A ``phylo`` object.
-# -log Whether the height of the phylogenetic tree should be log-transformed (log10(x + 1)).
-#
-# == details
-# The motivation is that phylogenetic tree may contain polytomies, which means at a certain node,
-# there are more than two children branches. Available tools that do the conversion only support binary trees.
-#
-# The returned ``dendrogram`` object is not in its standard format which means it can not be properly
-# drawn by the ``plot.dendrogram`` function. However, you can still apply dendextend::`dendextend::cutree` to the returned
-# ``dendrogram`` object with no problem and the dendrogram can be properly drawn with the ComplexHeatmap package.
-#
-# == value
-# A ``dendrogram`` object.
-#
-# == example
-# require(ape)
-# data(bird.families)
-# d = phylo_to_dendrogram(bird.families)
-#
-# require(ComplexHeatmap)
-# grid.dendrogram(d, test = TRUE)
+#' @details
+#' [`phylo_to_dendrogram()`] converts a `phylo` object to a `dendrogram` object.
+#' 
+#' The motivation is that phylogenetic tree may contain polytomies, which means at a certain node,
+#' there are more than two children branches. Available tools that do the conversion only support binary trees.
+#'
+#' The returned `dendrogram` object is not in its standard format which means it can not be properly
+#' drawn by the [`stats::plot.dendrogram()`] function. However, you can still apply [`stats::cutree()`] to the returned
+#' `dendrogram` object with no problem and the dendrogram can be properly drawn with the **ComplexHeatmap** package (see examples).
+#'
+#' @return A [`stats::dendrogram`] object.
+#' @rdname spiral_phylo
+#' @export
+#' @examples
+#' require(ape)
+#' data(bird.families)
+#' d = phylo_to_dendrogram(bird.families)
+#'
+#' ComplexHeatmap::grid.dendrogram(d, test = TRUE)
 phylo_to_dendrogram = function(obj, log = FALSE) {
     if(!inherits(obj, "phylo")) {
         stop_wrap("The input should be a 'phylo' object.")