artpoon/ggfree

ggplot2-style plots with base R graphics

ggfree's Issues

slopegraph could be generalized to parallel coordinates

credit: Norm Matloff for pointing this out
however, the MASS library already has an implementation of parallel coordinates via parcoord - worth the effort?

ridgeplot: can't set step to zero

Setting step to zero should cause all ridges to be plotted at the same level (relative to vertical axis). Instead we get an error:

Error in axis(side = 2, at = seq(step, n * step, step), labels = labels,  : 
  'at' and 'labels' lengths differ, 1 != 4

Make ridgeplots

slopegraph should automatically adjust shim for labels

Error while downloading ggfree package

@ArtPoon. I was trying to download the ggfree package and i got this error saying a file may be corrupted..

Downloading GitHub repo ArtPoon/ggfree@master
✔  checking for file ‘/tmp/RtmpifOPql/remotes28c9121cd011/ArtPoon-ggfree-a77c6b3/DESCRIPTION’ ...
─  preparing ‘ggfree’:
✔  checking DESCRIPTION meta-information ...
   Warning: /tmp/RtmplDOCZk/Rbuild31261b3e9c2a/ggfree/man/plot.phyloLayout.Rd:46: unexpected TEXT ' ', expecting '{'
   Warning: /tmp/RtmplDOCZk/Rbuild31261b3e9c2a/ggfree/man/tree.layout.Rd:13: unexpected TEXT ' ', expecting '{'
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘ggfree_0.1.0.tar.gz’
   
Installing package into ‘/home/abayomi/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘ggfree’ ...
** R
** data
*** moving datasets to lazyload DB
Warning: file ‘StJohns.RData’ has magic number 'RDX3'
  Use of save versions prior to 2 is deprecated
Error in load(zfile, envir = envir) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘ggfree’
* removing ‘/home/abayomi/R/x86_64-pc-linux-gnu-library/3.4/ggfree’
Error: Failed to install 'ggfree' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpifOPql/file28c92e2d4e6b/ggfree_0.1.0.tar.gz’ had non-zero exit status

stackplot: Incorporate baselines from Byron and Wattenberg

http://leebyron.com/streamgraph/stackedgraphs_byron_wattenberg.pdf

subtrees() is making as.phyloLayout slow

tree: rooting the tree might break count.tips()

Issue raised by user, need to confirm

stackplot: 'w' type is wrong

> require(ggfree)
> stackplot(cbc[2:n])

> stackplot(cbc[2:n], type='w')

> head(cbc)
  year American.Crow Canada.Goose Common.Goldeneye Common.Merganser
1 1960      3.393258  0.005617978        1.9494382         6.741573
2 1961      6.278027  0.000000000        0.3811659        26.905830
3 1962      2.590674  0.000000000        0.5699482         7.772021
4 1963      5.633803  0.000000000        1.0328638        23.474178
5 1964      8.823529  0.053921569        0.4901961        25.000000
6 1965     15.189873  0.000000000        1.1392405         4.493671
  European.Starling Greater.Scaup Herring.Gull House.Sparrow
1          7.303371    0.30337079    56.179775      18.53933
2         14.798206    0.11659193    53.811659      15.24664
3         21.761658    0.27461140    22.279793      10.36269
4         19.248826    0.35211268    14.553991      13.61502
5         20.588235    0.14705882     7.843137      14.70588
6         23.417722    0.05696203     7.594937      15.82278
  Long.tailed.Duck   Mallard
1       0.81460674 1.0898876
2       0.04932735 1.2107623
3       0.16580311 1.0362694
4       2.58215962 1.1267606
5       0.27941176 0.9803922
6       0.10759494 2.7848101
> tail(cbc)
   year American.Crow Canada.Goose Common.Goldeneye Common.Merganser
53 2012      2.544333     31.24647         5.864816        4.2508353
54 2013      2.585071     30.98793         3.408342        2.7497256
55 2014      4.284519     26.48257         7.609484        6.0195258
56 2015      3.085973     20.68326         7.013575        0.8642534
57 2016      3.027925     16.12739         9.665359        2.6171244
58 2017      1.997484     33.53459        10.968553        0.8201258
   European.Starling Greater.Scaup Herring.Gull House.Sparrow
53          11.51375     10.573117     4.718581      7.571318
54          73.62239      6.344676    12.749726      9.890231
55          46.53835     19.129707    12.686192      7.352859
56          24.33032      9.398190     1.936652     10.524887
57          19.42765     13.270252     3.803369     11.839372
58          14.30943      6.933333     1.569811     13.740881
   Long.tailed.Duck  Mallard
53         1.922385 26.99049
54        22.557629 24.28650
55        28.535565 15.49233
56        10.438914 13.06787
57        20.816986 15.99815
58        17.433962 25.32830

ridgeplot y-axis labeling is clumsy

Currently we are using an arbitrary numeric index to arrange densities along the y-axis. This causes problems if the labels are numeric, e.g., progressively increasing years.

Make donutplots

See ggsunburst

ridgeplot: cannot set step to 0

Throws the following error:

Error in axis(side = 2, at = seq(step, n * step, step), labels = labels,  : 
  'at' and 'labels' lengths differ, 1 != 3

Error in draw.clade: invalid subscript type 'list'

Attempting to color branches in very large tree:

> # all sequences
> phy <- read.tree("~/git/flu/data/removeX.ft2.nwk")
> phy <- midpoint(phy)
> phy <- ladderize(phy)
> pal <- gg.rainbow(18)
> # it takes a couple of minutes to generate this layout
> L <- tree.layout(phy)
> res <- 300
> png("~/git/flu/test.png", width=5*res, height=8*res, res=res)
> plot(L, label='n')
> for (i in 1:18) {
+   print(i)
+   # note phy$tip.label == L2$nodes$label[1:Ntip(phy)]
+   idx <- which(grepl(paste("\\(H", i, "[N)]", sep=""), phy$tip.label))
+   draw.clade(L, tips=phy$tip.label[idx], col=pal[i])
+   # label clades using tip farthest from origin
+   #last.tip <- idx[which.max(L2$nodes$r[idx])]
+ }
[1] 1
Error in obj$edges$y0[parents] : invalid subscript type 'list'

slopegraph changes par(mar), should revert back to user's settings

Need to save user's mar settings and then restore after plot.

as.phyloData fails for an annotated tree that was just unrooted

Here, phy is a tree that I simulated with twt, which annotates the S3 object with additional node and edge features. Unrooting the tree removes the root node and one edge, such that these additional features have the wrong length:

>   pd <- as.phyloData(phy, unscaled)
Warning messages:
1: In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute event.type of length 135
2: In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute compartment1 of length 135
3: In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute compartment2 of length 135
4: In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute type1 of length 135
5: In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute type2 of length 135

Proposed solution, overwrite unroot that is imported from the ape package.

Implement ggrepel-like label layout algorithm

This would be really nice to have...

Decorating a bird phylogeny with a numerical variable

Hi there,
Thank you for this, your code is amazing - I've been trying to use ggtree and have found the documentation really poor, for my particular task.

I'm trying to decorate a bird phylogeny (made with birdtree.org), and I'd like to decorate with another variable. My variable is the accuracy per species in an identification test, which I'd like to show with the phylogeny.

print(acc)

[1] 0.9277778 0.9438059 0.9272353 0.8306878 0.8876118 0.9082126 0.9476373 0.9053498 0.9333333
[10] 0.9449735 0.9487179 0.9656085 0.9317739 0.9272353 0.9444444 0.9225589 0.9382716 0.9469136
[19] 0.9583333

As you can see, it's not an integer. This was the code I used
`require(devtools)
devtools::install_github("ArtPoon/ggfree")

library(ggfree)
require(RColorBrewer)
L <- tree.layout(bird_tree, type='o')
plot(L, cex.lab=0.7, offset=2, mar=rep(5,4), col='chocolate')
image(L, z=as.matrix(acc), xlim=c(28.5,30), col=pal)`

However, the variable is misplaced inside the actual phylogeny

Contribute package to CRAN

Running R CMD check . raises 1 error, 9 warnings and 5 notes:

* using log directory ‘/home/art/git/ggfree/..Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggfree’ version ‘0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  vignettes/.gitignore
  ..Rcheck
  .git
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggfree’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/art/git/ggfree/man/plot.phyloLayout.Rd:45: unexpected TEXT ' ', expecting '{'
  Warning: /home/art/git/ggfree/man/tree.layout.Rd:13: unexpected TEXT ' ', expecting '{'
See ‘/home/art/git/ggfree/..Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directory with the name of a check directory:
  ./..Rcheck
Most likely, these were included erroneously.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.phyloData:
  function(obj)

print:
  function(x, ...)
print.phyloLayout:
  function(obj)

image:
  function(x, ...)
image.phyloLayout:
  function(obj, z, xlim, col, border, xaxt, ...)

lines:
  function(x, ...)
lines.phyloLayout:
  function(obj, col, shade, ...)

plot:
  function(x, ...)
plot.phyloLayout:
  function(obj, type, col, lwd, label, cex.lab, mar, ...)

points:
  function(x, ...)
points.phyloLayout:
  function(obj, ...)

text:
  function(x, ...)
text.phyloLayout:
  function(obj, label, align, cex.lab, offset, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.layout.equalangle: no visible global function definition for
  ‘is.rooted’
.layout.equalangle: no visible global function definition for ‘Nnode’
.layout.radial: no visible global function definition for ‘Ntip’
.layout.rect: no visible global function definition for ‘Ntip’
.layout.rect: no visible global function definition for ‘postorder’
add.alpha : <anonymous>: no visible global function definition for
  ‘col2rgb’
add.alpha : <anonymous>: no visible global function definition for
  ‘rgb’
add.grid: no visible global function definition for ‘par’
add.grid: no visible global function definition for ‘rect’
add.grid: no visible global function definition for ‘abline’
add.grid: no visible global function definition for ‘box’
add.scalebar: no visible global function definition for ‘segments’
add.scalebar: no visible global function definition for ‘text’
as.phyloData: no visible global function definition for ‘Nnode’
as.phyloData: no visible global function definition for ‘Ntip’
as.phyloData: no visible global function definition for ‘subtrees’
as.phyloData: no visible binding for global variable ‘Ntip’
as.phyloData: no visible global function definition for ‘node.depth’
as.phyloData: no visible global function definition for
  ‘node.depth.edgelength’
blend.colors: no visible global function definition for ‘col2rgb’
blend.colors: no visible global function definition for ‘rgb’
draw.arc: no visible global function definition for ‘lines’
draw.arc: no visible global function definition for ‘polygon’
draw.guidelines: no visible global function definition for ‘segments’
image.phyloLayout: no visible global function definition for
  ‘colorRampPalette’
image.phyloLayout: no visible global function definition for ‘par’
image.phyloLayout: no visible global function definition for ‘rect’
image.phyloLayout: no visible global function definition for ‘axis’
image.phyloLayout: no visible binding for global variable ‘geno’
lines.phyloLayout: no visible global function definition for ‘segments’
plot.phyloLayout: no visible global function definition for ‘par’
plot.phyloLayout: no visible global function definition for ‘plot’
plot.phyloLayout: no visible global function definition for ‘lines’
points.phyloLayout: no visible global function definition for ‘points’
polarplot: no visible global function definition for ‘plot’
polarplot: no visible binding for global variable ‘text’
print.phyloData: no visible global function definition for ‘str’
print.phyloData: no visible global function definition for ‘head’
print.phyloLayout: no visible global function definition for ‘head’
ridgeplot: no visible global function definition for ‘plot’
ridgeplot: no visible global function definition for ‘axis’
ridgeplot: no visible global function definition for ‘polygon’
ridgeplot: no visible global function definition for ‘lines’
ridgeplot: no visible global function definition for ‘segments’
ringplot: no visible global function definition for ‘par’
ringplot: no visible global function definition for ‘plot’
ringplot: no visible global function definition for ‘text’
slopegraph: no visible global function definition for ‘par’
slopegraph: no visible global function definition for ‘plot’
slopegraph: no visible global function definition for ‘axis’
slopegraph: no visible global function definition for ‘text’
slopegraph : <anonymous>: no visible global function definition for
  ‘lines’
slopegraph : <anonymous>: no visible global function definition for
  ‘text’
text.phyloLayout: no visible global function definition for ‘par’
text.phyloLayout: no visible global function definition for ‘text’
unroot: no visible global function definition for ‘is.rooted’
unroot: no visible global function definition for ‘Ntip’
unroot: no visible global function definition for ‘Nnode’
unroot: no visible global function definition for ‘unroot.phylo’
Undefined global functions or variables:
  Nnode Ntip abline axis box col2rgb colorRampPalette geno head
  is.rooted lines node.depth node.depth.edgelength par plot points
  polygon postorder rect rgb segments str subtrees text unroot.phylo
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "rgb")
  importFrom("graphics", "abline", "axis", "box", "lines", "par", "plot",
             "points", "polygon", "rect", "segments", "text")
  importFrom("utils", "head", "str")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: man/plot.phyloLayout.Rd:45: unexpected TEXT ' ', expecting '{'
prepare_Rd: man/tree.layout.Rd:13: unexpected TEXT ' ', expecting '{'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘flu’ ‘structSI’
Undocumented data sets:
  ‘flu’ ‘structSI’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add.alpha'
  ‘col’ ‘alpha’
Documented arguments not in \usage in documentation object 'add.alpha':
  ‘col:’ ‘alpha:’

Undocumented arguments in documentation object 'add.grid'
  ‘mode’ ‘fg.col’ ‘bg.col’ ‘lwd.major’ ‘lwd.minor’ ‘bty’
Documented arguments not in \usage in documentation object 'add.grid':
  ‘mode:’ ‘fg.col:’ ‘bg.col:’ ‘lwd.major:’ ‘lwd.minor:’

Undocumented arguments in documentation object 'add.scalebar'
  ‘obj’ ‘len’ ‘x0’ ‘y0’ ‘lwd’ ‘...’
Documented arguments not in \usage in documentation object 'add.scalebar':
  ‘obj:’ ‘len:’ ‘x0:’ ‘y0:’ ‘...:’

Undocumented arguments in documentation object 'as.phyloData'
  ‘phy’ ‘unscaled’
Documented arguments not in \usage in documentation object 'as.phyloData':
  ‘phy:’

Undocumented arguments in documentation object 'blend.colors'
  ‘col’
Documented arguments not in \usage in documentation object 'blend.colors':
  ‘col:’

Undocumented arguments in documentation object '.layout.equalangle'
  ‘phy’ ‘unscaled’

Undocumented arguments in documentation object 'draw.arc'
  ‘x’ ‘y’ ‘theta0’ ‘theta1’ ‘r0’ ‘r1’ ‘n’ ‘...’
Documented arguments not in \usage in documentation object 'draw.arc':
  ‘x:’ ‘y:’ ‘theta0:’ ‘theta1:’ ‘r0:’ ‘r1:’ ‘n:’

Undocumented arguments in documentation object 'draw.guidelines'
  ‘obj’ ‘lty’ ‘...’
Documented arguments not in \usage in documentation object 'draw.guidelines':
  ‘obj:’ ‘lty:’ ‘...:’

Undocumented arguments in documentation object 'image.phyloLayout'
  ‘obj’ ‘z’ ‘xlim’ ‘col’ ‘border’ ‘xaxt’ ‘...’
Documented arguments not in \usage in documentation object 'image.phyloLayout':
  ‘obj:’ ‘z:’ ‘xlim:’ ‘col:’ ‘border:’ ‘xaxt:’

Undocumented arguments in documentation object 'lines.phyloLayout'
  ‘obj’ ‘col’ ‘shade’ ‘...’
Documented arguments not in \usage in documentation object 'lines.phyloLayout':
  ‘obj:’ ‘col:’ ‘shade:’ ‘...:’

Undocumented arguments in documentation object 'plot.phyloLayout'
  ‘obj’ ‘type’ ‘col’ ‘lwd’ ‘label’ ‘cex.lab’ ‘mar’ ‘...’
Documented arguments not in \usage in documentation object 'plot.phyloLayout':
  ‘obj:’ ‘type:’ ‘col:’ ‘lwd:’ ‘label:’ ‘cex.lab:’ ‘mar:’ ‘...:’

Undocumented arguments in documentation object 'points.phyloLayout'
  ‘obj’ ‘...’
Documented arguments not in \usage in documentation object 'points.phyloLayout':
  ‘obj:’ ‘...:’

Undocumented arguments in documentation object 'polarplot'
  ‘obj’ ‘x’ ‘y’ ‘r’ ‘theta’ ‘space’ ‘col’ ‘use.names’ ‘pad.names’
  ‘cex.names’ ‘...’
Documented arguments not in \usage in documentation object 'polarplot':
  ‘obj:’ ‘r:’ ‘theta:’ ‘space:’ ‘col:’ ‘use.names:’ ‘pad.names:’
  ‘cex.names:’ ‘...:’

Undocumented arguments in documentation object 'print.phyloData'
  ‘obj’
Documented arguments not in \usage in documentation object 'print.phyloData':
  ‘obj:’

Undocumented arguments in documentation object 'print.phyloLayout'
  ‘obj’
Documented arguments not in \usage in documentation object 'print.phyloLayout':
  ‘obj:’

Undocumented arguments in documentation object 'ridgeplot'
  ‘x’ ‘xlim’ ‘labels’ ‘yaxt’ ‘xlab’ ‘ylab’ ‘step’ ‘col’ ‘fill’ ‘lwd’
  ‘density.args’ ‘add.grid’ ‘grid.args’ ‘extend.lines’ ‘add’ ‘...’
Documented arguments not in \usage in documentation object 'ridgeplot':
  ‘x:’ ‘xlim:’ ‘labels:’ ‘xlab:’ ‘ylab:’ ‘step:’ ‘col:’ ‘fill:’ ‘lwd:’
  ‘density.args:’ ‘add.grid:’ ‘grid.args:’ ‘extend.lines:’ ‘add:’
  ‘...:’

Undocumented arguments in documentation object 'ringplot'
  ‘vec’ ‘r0’ ‘r1’ ‘theta’ ‘x’ ‘y’ ‘col’ ‘use.names’ ‘offset’ ‘srt’
  ‘cex.label’ ‘...’
Documented arguments not in \usage in documentation object 'ringplot':
  ‘vec:’ ‘r0:’ ‘r1:’ ‘theta:’ ‘x:’ ‘y:’ ‘col:’ ‘use.names:’ ‘offset:’
  ‘srt:’ ‘cex.label:’ ‘...:’

Undocumented arguments in documentation object 'slopegraph'
  ‘x’ ‘y’ ‘type’ ‘names.arg’ ‘xlab’ ‘ylab’ ‘colorize’ ‘pal’ ‘shim’
  ‘cex.text’ ‘...’
Documented arguments not in \usage in documentation object 'slopegraph':
  ‘x:’ ‘y:’ ‘type:’ ‘names.arg:’ ‘xlab:’ ‘ylab:’ ‘colorize:’ ‘pal:’
  ‘shim:’ ‘cex.text:’ ‘...:’

Undocumented arguments in documentation object 'text.phyloLayout'
  ‘obj’ ‘label’ ‘align’ ‘cex.lab’ ‘offset’ ‘...’
Documented arguments not in \usage in documentation object 'text.phyloLayout':
  ‘obj:’ ‘label:’ ‘align:’ ‘cex.lab:’ ‘...:’

Undocumented arguments in documentation object 'tree.layout'
  ‘phy’ ‘type’ ‘unscaled’
Documented arguments not in \usage in documentation object 'tree.layout':
  ‘phy:’ ‘type:’ ‘unscaled:’

Undocumented arguments in documentation object 'unroot'
  ‘obj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' calls not declared from:
  ‘HistData’ ‘RColorBrewer’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘ggfree-trees.Rmd’, ‘ggfree-trees.md’,
    ‘man/figures/README-unnamed-chunk-10-1.png’,
    ‘man/figures/README-unnamed-chunk-10-2.png’,
    ‘man/figures/README-unnamed-chunk-11-1.png’,
    ‘man/figures/README-unnamed-chunk-14-1.png’,
    ‘man/figures/README-unnamed-chunk-14-2.png’,
    ‘man/figures/README-unnamed-chunk-14-3.png’,
    ‘man/figures/README-unnamed-chunk-2-1.png’,
    ‘man/figures/README-unnamed-chunk-4-1.png’,
    ‘man/figures/README-unnamed-chunk-5-1.png’,
    ‘man/figures/README-unnamed-chunk-7-1.png’,
    ‘man/figures/README-unnamed-chunk-8-1.png’,
    ‘man/figures/README-unnamed-chunk-9-1.png’
* checking examples ... ERROR
Running examples in ‘ggfree-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.phyloLayout
> ### Title: plot.phyloLayout
> ### Aliases: plot.phyloLayout
> 
> ### ** Examples
> 
> # generate random coalescent tree
> set.seed(1999); phy <- rcoal(50)
> 
> # rectangular tree
> plot(tree.layout(phy, type='r'), mar=c(3,0,0,1))
> axis(side=1)
> 
> # unscaled slanted tree with colors
> pal <- colorRampPalette(c('cadetblue', 'brown'))
> plot(tree.layout(phy, type='s', unscaled=T), col=pal(5))
Error in as.phyloData(phy, unscaled) : T used instead of TRUE
Calls: plot -> tree.layout -> .layout.rect -> as.phyloData
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
dir.exists(dir) is not TRUE
Package vignette without corresponding single PDF/HTML:
   ‘ggfree-trees.Rmd’

* checking running R code from vignettes ... NONE
  ‘ggfree-trees.Rmd’using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 9 WARNINGs, 5 NOTEs

Add matrix rotation for tree layouts

Add radar/spider plots

Should be fairly straight-forward - these seem to be translucent polygons over a radial layout (which is in itself a weird mix of coordinate systems).

Problems loading lazydata on cmd line

art@Kestrel:~/git/ggfree$ R CMD INSTALL .
* installing to library ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6’
* installing *source* package ‘ggfree’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Warning: file ‘co2.RData’ has magic number 'X'
  Use of save versions prior to 2 is deprecated
Error in load(zfile, envir = tmp_env) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘ggfree’
* removing ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6/ggfree’
* restoring previous ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6/ggfree’

I've run into this problem before working with different versions of R (RData version 2 is deprecated post 3.5) but in this case it is all local (same versoin of R, 3.6.1).

MODEL$new does not accept yaml with empty `pieces`

> mod <- MODEL$new(settings)
Error in matrix(nrow = length(pieces), ncol = 6, dimnames = list(1:length(pieces),  : 
  length of 'dimnames' [1] not equal to array extent

Here the settings came from a YAML with no pieces entry

phangorn midpoint breaks tree.layout

> njtree <- midpoint(njtree)
> L <- tree.layout(njtree, type='o')
> plot(L, label='n')
 Error in plot.window(...) : need finite 'xlim' values 

tree: draw.clade doesn't work for rectangular layout

This is a tree I reconstructed from some SARS-CoV-2 genomes:

> phy <- read.tree('~/git/covizu/data/timetree.nwk')
> phy

Phylogenetic tree with 263 tips and 177 internal nodes.

Tip labels:
  B.6.1, B.5, B.17, B.4, B.4.1, B.4.2, ...
Node labels:
  NODE_0000002, NODE_0000215, NODE_0000216, NODE_0000217, NODE_0000222, NODE_0000223, ...

Rooted; includes branch lengths.

This works fine for unrooted tree layout:

> tips <- c("B.5", 'B.2.1', 'B.9')
> L <- tree.layout(phy, 'u')
> plot(L)
> draw.clade(L, tips, lwd=2)

But it messes up for rect layout:

> L <- tree.layout(phy, 'r')
Warning message:
In as.phyloData(phy, unscaled) :
  as.phyloData ignoring attribute root.edge of length 1
> plot(L)
> draw.clade(L, tips, lwd=2)

tree: color labels don't work for circular layout

MRE:

require(ggfree)
set.seed(1)
phy <- rtree(50)
L <- tree.layout(phy)
col <- ifelse(grepl("t1", L$nodes$label), 'red', 'blue')
plot(L, label='n')
text(L, align=F, col=col, cex=0.8)

L2 <- tree.layout(phy, type='o')
col <- ifelse(grepl("t1", L2$nodes$label), 'red', 'blue')
plot(L2, label='n')
text(L2, align=F, col=col, cex=0.8)

Reported by @veratai

Maintain a "see also" section in README

For R packages authored and maintained by others that provide nice viz options without ggplot2, e.g., beeswarm.

Incorrect branch lengths from unrooted (equal angle) layout

Something's wrong with the equal layout algorithm.
When unscaled=FALSE (default), the branch lengths should be unaffected (mapping x from rectangular layout directly to radius parameter r).
However, it doesn't look like this is getting handled correctly.

ridgeplot fails if user passes vector instead of list

> ridgeplot(rnorm(100))
Error in ridgeplot(rnorm(100)) : 
  Unsupported class of argument x (must be list)

Expected response: generate a ridgeplot with a single density.

Passing `log='y'` to slopegraph() throws warnings

> slopegraph(t(df[1:2, taxa]), names.arg=c('sample1', 'sample2'), log='y')
There were 12 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In plot.xy(xy.coords(x, y), type = type, ...) :
  "log" is not a graphical parameter
2: In plot.xy(xy.coords(x, y), type = type, ...) :
  "log" is not a graphical parameter

ridgeplot needs to handle missing vectors

Came across this when attempting to add a second series of densities to the current plot - one of the entries in the list did not exist.

Possible strategies:

1. allow user to set NA as placeholder - problem density doesn't like missing (non-numeric) values.
2. match densities using list names. problem what if the user wants to send an unnamed list? What if the names are not exactly the same, but the data are comparable?

ringplot is squished if plot area is not square

Need to detect the dimensions of the plot device before specifying the xlim and ylim ranges