GNU bug report logs - #57341
gnu: Add r-ggvenndiagram and r-rvenn.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: gnu: Add r-ggvenndiagram and r-rvenn.
Date: Mon, 22 Aug 2022 12:11:05 +0000

[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Message #8 received at 57341 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <57341 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-ggvenndiagram.
Date: Mon, 22 Aug 2022 14:14:41 +0200

* gnu/packages/cran.scm (r-ggvenndiagram): New variable.
---
 gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2091c258ec..b0debc99ba 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1097,6 +1097,45 @@ (define-public r-ggrastr
 scale-sensitive information.")
     (license license:expat)))
 
+(define-public r-ggvenndiagram
+  (package
+    (name "r-ggvenndiagram")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggVennDiagram" version))
+       (sha256
+        (base32
+         "1mjs488npnxd53nsw936iw2vzv7z38h8d02pm4lwrz4i83jg3www"))))
+    (properties `((upstream-name . "ggVennDiagram")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dplyr
+           r-ggplot2
+           r-magrittr
+           r-plotly
+           r-purrr
+           r-rvenn
+           r-sf
+           r-stringr
+           r-tibble))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/gaospecial/ggVennDiagram")
+    (synopsis "Implementention of the Venn diagram using ggplot2")
+    (description
+     "This package implements easy-to-use functions to generate 2-7 sets Venn plot
+in publication quality.  @code{ggVennDiagram} plot Venn using well-defined geometry
+dataset and @code{ggplot2}.  The shapes of 2-4 sets Venn use circles and ellipses,
+while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which
+are developed and imported from another package @code{venn}.  We provide internal
+functions to integrate shape data with user provided sets data, and calculated
+the geometry of every regions/intersections of them, then separately plot Venn
+in three components: set edges, set labels, and regions.  From version 1.0, it
+is possible to customize these components as you demand in ordinary @code{ggplot2}
+grammar.")
+    (license license:gpl3)))
+
 (define-public r-lmds
   (package
     (name "r-lmds")
-- 
2.37.2

Message #11 received at 57341 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <57341 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-rvenn.
Date: Mon, 22 Aug 2022 14:14:40 +0200

* gnu/packages/cran.scm (r-rvenn): New variable.
---
 gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e03b707162..2091c258ec 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -749,6 +749,42 @@ (define-public r-v8
 WebAssembly engine.")
     (license license:expat)))
 
+(define-public r-rvenn
+  (package
+    (name "r-rvenn")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RVenn" version))
+       (sha256
+        (base32
+         "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4"))))
+    (properties `((upstream-name . "RVenn")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggforce
+           r-ggplot2
+           r-magrittr
+           r-pheatmap
+           r-purrr
+           r-rlang
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=RVenn")
+    (synopsis "Set operations for many sets")
+    (description
+     "The base functions for set operations in @code{R} can be used for only two
+sets.  This package @code{RVenn} provides functions for dealing with multiple sets.
+It uses @code{purr} to find the union, intersection and difference of three or
+more sets.  This package also provides functions for pairwise set operations among
+several sets.  Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram
+can be drawn for two or three sets.  For bigger data sets, a clustered heatmap
+showing the presence or absence of the elements of the sets can be drawn based on
+the @code{pheatmap} package.  Finally, enrichment test can be applied to two sets
+whether an overlap is statistically significant or not.")
+    (license license:gpl3)))
+
 (define-public r-dot
   (package
     (name "r-dot")

base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90
-- 
2.37.2

Message #16 received at 57341-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 57341-done <at> debbugs.gnu.org
Subject: Re: [bug#57341] [PATCH 1/2] gnu: Add r-rvenn.
Date: Tue, 23 Aug 2022 12:05:50 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-rvenn): New variable.
[…]
> * gnu/packages/cran.scm (r-ggvenndiagram): New variable.

I applied both.  Thanks!

-- 
Ricardo

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