Update of Venn diagrams, introduction of Polyominoes and graph representation #2

smoe · 2020-03-03T14:11:00Z

This PR is the same as r-gregmisc/r-gregmisc#3 with improvements to venn(), polyominoes and the graph representation.

Transparency and coloring for classical Venn diagrams, introducing Polyominoes and graph representation.

smoe · 2020-03-10T22:23:36Z

What I could also think of is a function that generates functions. That way you would only need to export that generator. But does that not complicate it all?

arni-magnusson · 2020-03-14T20:50:55Z

Hi Steffen, thanks for the pull request. A package check results in 6 warnings and 3 notes. Do you also get these on your machine?

$ R --vanilla CMD build --compact-vignettes --resave-data gplots
$ R --vanilla CMD check --as-cran gplots_3.1.0.tar.gz

* using log directory ‘/home/arnima/git/smoe/gplots.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘gplots/DESCRIPTION’ ... OK
* this is package ‘gplots’ version ‘3.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Gregory Warnes <greg@warnes.net>’

New maintainer:
  Gregory Warnes <greg@warnes.net>
Old maintainer(s):
  Tal Galili <tal.galili@gmail.com>
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘gplots’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘igraph’
'library' or 'require' calls not declared from:
  ‘RColorBrewer’ ‘igraph’
'loadNamespace' or 'requireNamespace' call not declared from: ‘igraph’
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘igraph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.venn.graph:
  function(data, col, col.scheme, col.function, add, debug, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  plot.venn.graph plot.venn.polyominoes
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
drawVennDiagram: no visible binding for global variable ‘type’
drawVennDiagram: no visible global function definition for
  ‘drawVennGraph’
drawVennPolyominoes: no visible binding for global variable ‘rainbow’
drawVennPolyominoes: no visible global function definition for
  ‘colorRampPalette’
drawVennPolyominoes: no visible global function definition for ‘head’
plot.venn.graph: no visible binding for global variable ‘rainbow’
plot.venn.graph: no visible global function definition for ‘V’
plot.venn.graph: no visible global function definition for ‘V<-’
plot.venn.polyominoes: no visible binding for global variable ‘rainbow’
venn.graph.colouring: no visible binding for global variable ‘rainbow’
venn.graph.colouring: no visible global function definition for ‘V’
venn.graph.simplify: no visible global function definition for ‘V’
venn.graph.simplify: no visible global function definition for
  ‘delete.vertices’
vennMembers: no visible global function definition for ‘head’
Undefined global functions or variables:
  V V<- colorRampPalette delete.vertices drawVennGraph head rainbow
  type
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘drawVennPolyominoes.colouring.featureCount’
  ‘drawVennPolyominoes.colouring.pValue’
  ‘drawVennPolyominoes.fields.labels.binary’
  ‘drawVennPolyominoes.fields.labels.letter’ ‘plot.venn.graph’
  ‘plot.venn.polyominoes’ ‘venn.graph.colouring’ ‘venn.graph.simplify’
  ‘venn.observed2expected’
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 ... WARNING
Codoc mismatches from documentation object 'venn':
venn
  Code: function(data, universe = NA, small = 0.7, showSetLogicLabel =
                 FALSE, simplify = FALSE, show.plot = TRUE,
                 intersections = TRUE, graph = FALSE, names = NULL,
                 statistics = NULL, n.perm = 100, ...)
  Docs: function(data, universe = NA, small = 0.7, showSetLogicLabel =
                 FALSE, simplify = FALSE, show.plot = TRUE,
                 intersections = TRUE, names, ...)
  Argument names in code not in docs:
    graph statistics n.perm
  Mismatches in argument names:
    Position: 8 Code: graph Docs: names
    Position: 9 Code: names Docs: ...
  Mismatches in argument default values:
    Name: 'names' Code: NULL Docs:
plot.venn
  Code: function(x, y, ..., small = 0.7, showSetLogicLabel = FALSE,
                 simplify = FALSE, type = "regular", col = NA, density
                 = NULL, border = NULL, angle = NA, lty = par("lty"),
                 debug = F)
  Docs: function(x, y, ..., small = 0.7, showSetLogicLabel = FALSE,
                 simplify = FALSE)
  Argument names in code not in docs:
    type col density border angle lty debug

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘venn.pdf’ from 824Kb to 473Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘heatmap2Test.R’
  Comparing ‘heatmap2Test.Rout’ to ‘heatmap2Test.Rout.save’ ... OK
  Running ‘heatmap_to_heatmap.2_test.R’
  Running ‘plotmeans_nobars.R’
  Running ‘test_plottingDeepDendrogram.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘igraph’
'library' or 'require' calls not declared from:
  ‘RColorBrewer’ ‘igraph’
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
--- re-building ‘venn.Rnw’ using Sweave

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Warning in drawVennCircles(data, small = small, showSetLogicLabel = showSetLogicLabel,  :
  Not shown: 000 contains 1373

Warning in drawVennCircles(data, small = small, showSetLogicLabel = showSetLogicLabel,  :
  Not shown: 000 contains 1373


Error: processing vignette 'venn.Rnw' failed with diagnostics:
 chunk 9
Error in library(RColorBrewer) :
  there is no package called ‘RColorBrewer’

--- failed re-building ‘venn.Rnw’

SUMMARY: processing the following file failed:
  ‘venn.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 6 WARNINGs, 3 NOTEs
See
  ‘/home/arnima/git/smoe/gplots.Rcheck/00check.log’
for details.

smoe · 2020-03-28T18:02:40Z

Dear @warnes , dear @arni-magnusson ,
I just cloned

git clone https://github.com/smoe/gplots

and then ran

$ R CMD check .
* using log directory ‘/home/moeller/git/gplots/..Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... OK
* this is package ‘gplots’ version ‘3.0.3’
* 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:
  ..Rcheck
  .git
  .Rproj.user
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 ‘gplots’ can be installed ... OK
* 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 ... OK
* 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  boxplot.n plot.lm2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘r2d2’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘heatmap_to_heatmap.2_test.R’
  Running ‘heatmap2Test.R’
  Comparing ‘heatmap2Test.Rout’ to ‘heatmap2Test.Rout.save’ ...100c100
<  $ call         : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green",      margins = c(5, 10), ColSideColo| __truncated__ ...
---
>  $ call         : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green",      margins = c(5, 10), ColSideColors = cc, RowSideColors = rc, density.info = "density",  ...
  Running ‘plotmeans_nobars.R’
  Running ‘test_plottingDeepDendrogram.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Failed to locate the ‘weave’ output file (by engine ‘utils::Sweave’) for vignette with name ‘venn’. The following files exist in directory ‘/home/moeller/git/gplots/inst/doc’: ‘BalloonPlot.pdf’
Package vignette without corresponding single PDF/HTML:
   ‘venn.Rnw’

* checking running R code from vignettes ...
  ‘venn.Rnw’... OK
 OK
* checking re-building of vignette outputs ...Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
Warning in file.copy(pkgdir, vd2, recursive = TRUE) : too deep nesting
 OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
  ‘/home/moeller/git/gplots/..Rcheck/00check.log’
for details.

which except from this PDF thingy seems ... ok enough? But I then also noted that I was not in my master branch but defaulted into "developer". Master was "develop" plus a merge from your repository. And now I immediately ran into

* using log directory ‘/home/moeller/git/gplots/..Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... ERROR
Required fields missing or empty:
  ‘Author’ ‘Maintainer’
* DONE

Status: 1 ERROR
See
  ‘/home/moeller/git/gplots/..Rcheck/00check.log’
for details.

This error seems to be because for the neat new layout in the DESCRIPTION - a bit weird that this was not passed.

I had fixed some ugly bits like lines ending with blanks etc on the master branch after I merged (should have done that before, admittedy). And I also eliminated tabs when I felt that this was not in sync with how you did things, but otherwise ... it should work.

Could you please add https://cran.r-project.org/web/packages/RColorBrewer/index.html and try again? I promise to contribute a Vignette for boxplot. And a second one for heatmap if you merge it in so I can remove all the local branches of it all and work on your codebase again.

Directions on what I should do are welcome. I wish you would merge and we can clean things up together.

warnes

What I could also think of is a function that generates functions. That way you would only need to export that generator. But does that not complicate it all?

At the very least we should shorten the names as much as possible, as well as changing all of the dots to underscore so that we don't confuse the s3 object system.

I think we can probably make things easier on the users via couple of simple changes, similar how ggplots2 handles the multiplicity of functions:

Abbreviate drawVennPolyominoes. to dvp_, which shortens the names substantially: drawVennPolyominoes.fields.labels.letter to dvp_fields.labels.letter
Combine some of the individual functions into "generics", like drawVennPolyominoes.fields.labels.letter to dvp_fields(labels="letter").

Side note, I wonder how many people accidentally install gplots when they are looking for ggplot2 or vice versa? What kind of ruckus would it be if we created a package named gplots2 that simply displayed a wikipedia like "disambiguation" message listing both gplots and ggplots2 with appropriate links? 🤪

warnes · 2020-03-06T21:42:04Z

R/plot.venn.R

+                      debug=F
+                     )
+{
+  if (!is.matrix(x)) stop("Please have a true matrix passed to the 'plot.venn' method.")


This can probably be simplified to

stop("`x` should be a matrix.")

warnes · 2020-03-06T21:43:25Z

R/plot.venn.R

  }

+  if (is.list(type)) {
+      for (type.iterator in type) {
+          plot.venn(x=x,y=y,small=small,showSetLogicLabel=showSetLogicLabel,simplify=simplify,type=type.iterator)


Please run this through a code formatter to make it easier to read.

I agree with Greg's comments and have also been working on improvements on smoe/gplots to solve 4 Warnings and 1 Note (from 6W+3N down to 2W+2N).

See smoe#1.

Substantial work remains to be done on smoe/gplots to solve the pending warnings and notes, in addition to Greg's comments. Unfortunately, I may not be able to commit much more work to that, but it looks like the warnings and notes are quite accurate and pinpoint exactly what needs to be improved.

arni-magnusson

General comments: #2 (comment)

Suggested code improvements: smoe#1

smoe · 2020-03-29T17:58:53Z

I'll check. I also like the suggestions. Have you all contributed back your changes to the smoe/master branch? My next thing to do will be the renaming and this might be annoying to merge with whatever you have fixed locally.

arni-magnusson · 2020-03-29T18:16:48Z

That's right, smoe#1 adds six commits to smoe/gplots@master. The renaming of the plot.venn.graph and plot.venn.polyominoes functions will indeed solve one of the remaining notes.

Solve 4 warnings and 1 note

Eliminated one WARNING of R CMD check

smoe · 2020-03-30T03:05:46Z

It is down to 5 notes now.

$ R --vanilla CMD check --as-cran gplots_3.1.0.tar.gz
* using log directory ‘/home/moeller/git/gplots/gplots.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘gplots/DESCRIPTION’ ... OK
* this is package ‘gplots’ version ‘3.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Gregory Warnes <greg@warnes.net>’

New maintainer:
  Gregory Warnes <greg@warnes.net>
Old maintainer(s):
  Tal Galili <tal.galili@gmail.com>

Size of tarball: 11843589 bytes
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘gplots’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘gplots_3.1.0.tar.gz’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.venn.graph plot.venn.polyominoes
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘r2d2’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'venn':
  ‘plot.venn.graph’ ‘plot.venn.polyominoes’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘heatmap_to_heatmap.2_test.R’
  Running ‘heatmap2Test.R’
  Comparing ‘heatmap2Test.Rout’ to ‘heatmap2Test.Rout.save’ ... OK
  Running ‘plotmeans_nobars.R’
  Running ‘test_plottingDeepDendrogram.R’ [11s/11s]
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/moeller/git/gplots/gplots.Rcheck/00check.log’
for details.

To maintain sanity of S3 registry

smoe · 2020-04-01T00:30:52Z

I have now eliminated the warnings and the Venn-associated notes, also function names have been shortened. Please kindly have another look.

smoe · 2020-04-22T13:38:16Z

Hello,
Where are we with it all? It is my understanding that I have addressed all pending issues.
Best,
Steffen

arni-magnusson · 2020-04-24T12:22:42Z

The documentation of these functions needs improvement:

plotVennGraph
plotVennPolyominoes

According to the help page, they take the same x input as venn but that is not the case. Also, the help page implies that the output value of all three functions is identical, but that's not quite the case.

Overall, the help page is rather convoluted, mixing different input types and arguments. Is the y (ignored) useful? I think it might be easier for the user to understand these functions if each of them has a dedicated help page with examples. That way, the description field will also clarify the purpose of each function.

The help page also includes pV_draw. This function is not exported to users and I'm not sure if it should have a dedicated help page or not.

arni-magnusson · 2020-04-24T12:26:24Z

It would be helpful if you can draft a NEWS entry for plotVennGraph and plotVennPolyominoes. Are these the two Venn-related functions that should be described at the NEWS level?

I'm guessing the others are just helper functions that you would like to be exported for users to explore,

pV_colouringFeatureCount
pV_colouringPValue
pV_fieldsLabelsBinary
pV_fieldsLabelsLetter
venn.graph.colouring
venn.graph.simplify
venn.observed2expected

along with

pv_draw

if that's exported.

smoe · 2020-04-24T14:24:17Z

Thank you, @arni-magnusson .

The help page also includes pV_draw. This function is not exported to users and I'm not sure if it should have a dedicated help page or not.

I lost my oversight about "what is what and what is how important". Will review and update.

smoe

Isn't this all long done?

smoe · 2022-02-24T22:56:47Z

Hello again, I just checked on smoe@c581d35 and from what see and understand, this has all been addressed. Could you please have another look?

arni-magnusson · 2022-02-25T00:13:45Z

Hi Steffen! Yes, probably all done :)

I was cleaning up my workspace and removing lots of redundant forked repos. Before deleting anything, I wanted to compare things, and in the process I may have accidentally revived an obsolete pull request.

Just as well, I guess, to break the silence :) I'm curious to know about whether the plan is for Tal Galili to maintain the gplots package, and whether we plan to combine development from https://github.com/talgalili/gplots and https://github.com/r-gregmisc/gplots. I'll post a separate issue where we can maybe discuss that.

smoe · 2022-02-25T00:18:11Z

Hi Arni, thank you, please keep me in sync. We have deprived the scientific community from those venn graphs for the last two years. I feel bad. The "done" referred to me having reacted to all your request - you have not merged this, yet. You may want to consider to reopen my PR.

arni-magnusson · 2022-02-25T00:36:48Z

All systems green and go, as far as I am concerned :)
I think Greg would be the right person to merge.

smoe · 2022-02-25T00:40:12Z

Greg @warnes is our man, indeed. On my side I see the "Changes requested" still shining in some bright red color. Is there a way that you click on "approve" or so to leave only Greg's? Btw, I hope you are all fine.

arni-magnusson

Not able to review thoroughly, sorry about that.

Looks fine from a distance :) Approved review from my side.

smoe changed the title ~~Master~~ Update of Venn diagrams, introduction of Polyominoes and graph representation Mar 3, 2020

Extension of Venn diagrams

1c43e58

Transparency and coloring for classical Venn diagrams, introducing Polyominoes and graph representation.

smoe force-pushed the master branch from 135fe34 to 1c43e58 Compare March 3, 2020 14:42

smoe changed the base branch from develop to master March 3, 2020 14:45

warnes requested review from arni-magnusson and warnes March 5, 2020 22:46

warnes self-assigned this Mar 5, 2020

warnes added the enhancement New feature or request label Mar 5, 2020

warnes requested changes Mar 29, 2020

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Arni Magnusson added 6 commits March 29, 2020 18:34

Optimize PNG files for vignette

2fb4750

Import igraph

8ca5d0b

Suggest RColorBrewer

3231bbe

First arg in plot.venn.graph() is x, to align with generic plot()

e80eb71

Pass 'type' to drawVennDiagram()

3df8450

Bump date to suppress R CMD check note

f290d3f

arni-magnusson requested changes Mar 29, 2020

View reviewed changes

smoe and others added 6 commits March 29, 2020 20:28

Merge pull request #1 from arni-magnusson/smoe-help

11750f8

Solve 4 warnings and 1 note

Extended NAMESPACE as instructed by R CMD check

7e385a5

Renamed first argument to x, adjusted man page to code

b051dbc

Eliminated one WARNING of R CMD check

Shortening 'stop' message

07b3883

Applied R formatter

49adf68

Completed basic manual pages

4260c9d

smoe added 2 commits April 1, 2020 01:38

Changed .dot notation to camel case

51f6869

To maintain sanity of S3 registry

Shortening of function names.

c581d35

smoe requested review from arni-magnusson and warnes April 22, 2020 13:29

smoe commented Feb 24, 2022

View reviewed changes

arni-magnusson closed this Feb 25, 2022

arni-magnusson reopened this Feb 25, 2022

arni-magnusson approved these changes Feb 25, 2022

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Update of Venn diagrams, introduction of Polyominoes and graph representation #2

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Update of Venn diagrams, introduction of Polyominoes and graph representation #2

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