From patchwork Mon Aug 22 12:14:40 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 41868 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0A1F827BBEA; Mon, 22 Aug 2022 13:16:22 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A068227BBE9 for ; Mon, 22 Aug 2022 13:16:21 +0100 (BST) Received: from localhost ([::1]:32864 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oQ6Ls-00066e-R5 for patchwork@mira.cbaines.net; Mon, 22 Aug 2022 08:16:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34730) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ6Lb-00064M-5Y for guix-patches@gnu.org; Mon, 22 Aug 2022 08:16:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:48508) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oQ6La-0006ZG-KF for guix-patches@gnu.org; Mon, 22 Aug 2022 08:16:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oQ6La-0001yT-FL; Mon, 22 Aug 2022 08:16:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#57341] [PATCH 1/2] gnu: Add r-rvenn. References: <2a2d3263e6e74fc3a699a46a25dc5959@mdc-berlin.de> In-Reply-To: <2a2d3263e6e74fc3a699a46a25dc5959@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Mon, 22 Aug 2022 12:16:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 57341 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <57341@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 57341-submit@debbugs.gnu.org id=B57341.16611705141711 (code B ref 57341); Mon, 22 Aug 2022 12:16:02 +0000 Received: (at 57341) by debbugs.gnu.org; 22 Aug 2022 12:15:14 +0000 Received: from localhost ([127.0.0.1]:38254 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ6Kn-0000QB-SL for submit@debbugs.gnu.org; Mon, 22 Aug 2022 08:15:14 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:42357) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ6Kh-0008Cp-9C for 57341@debbugs.gnu.org; Mon, 22 Aug 2022 08:15:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1661170500; x=1662984901; bh=uypFV+TEgj+wyVQ 3CPkCfxvz+NL/Vyz/3tuHb/TNqaU=; b=AbfsbLxWez2akP9buZ9TbGFSdVKdQwq pQt9g7UHdHAEMG3xyOTcY0oth4gBdFhwEX3FFKsqWP6W+Y1YHlq7G/Dj5TflJyGq tgkMO8dkouftt08LkbLJqWGVePeHON7mmDJys9STPoSGs2nip8VHGZhm4rkjR89o OGLIjirbNc2w= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 27B0E300259 for <57341@debbugs.gnu.org>; Mon, 22 Aug 2022 14:14:57 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.12; Mon, 22 Aug 2022 14:14:56 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 22 Aug 2022 14:14:40 +0200 Message-ID: <20220822121441.2235-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.2 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-AS-Result: No-10--3.158900-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJ2G t3BMHXyaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/kwFzTzcgzhJYaGUdeitddqbs +nJ/tFJE/jpOn/YFJRcKI1JPpcUiZf1Oy/Axrj3Kqh5pv1eDPz7+a+v4FF31uU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DBR94Ea/yjStZ4g4hGKnWQ+toP9lAw/s4Su15 tqF9cquohQaieY4vKjb9PHtsjxvHGQwPtPHVYUrUx9ukNeKCVZMkIdU3Toq79xSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.158900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-SNTS-SMTP: CE10BEA764334001306AA77A69325C6BCF4FE86CCBF582D3DA849D127A1871422002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-rvenn): New variable. --- gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90 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") From patchwork Mon Aug 22 12:14:41 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 41867 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 80DD327BBE9; Mon, 22 Aug 2022 13:16:20 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 353A627BBE9 for ; Mon, 22 Aug 2022 13:16:20 +0100 (BST) Received: from localhost ([::1]:32862 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oQ6Lr-00066X-A8 for patchwork@mira.cbaines.net; Mon, 22 Aug 2022 08:16:19 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34728) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ6Lb-00064L-5P for guix-patches@gnu.org; Mon, 22 Aug 2022 08:16:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:48506) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oQ6La-0006ZF-CQ for guix-patches@gnu.org; Mon, 22 Aug 2022 08:16:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oQ6La-0001yI-3U; Mon, 22 Aug 2022 08:16:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#57341] [PATCH 2/2] gnu: Add r-ggvenndiagram. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Mon, 22 Aug 2022 12:16:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 57341 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <57341@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 57341-submit@debbugs.gnu.org id=B57341.1661170510683 (code B ref 57341); Mon, 22 Aug 2022 12:16:02 +0000 Received: (at 57341) by debbugs.gnu.org; 22 Aug 2022 12:15:10 +0000 Received: from localhost ([127.0.0.1]:38252 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ6Kj-0000AE-Cx for submit@debbugs.gnu.org; Mon, 22 Aug 2022 08:15:09 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:56611) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ6Kh-0008D8-9B for 57341@debbugs.gnu.org; Mon, 22 Aug 2022 08:15:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1661170501; x=1662984902; bh=YAs6xzxP6ZkEJg8Kh+/fBxoK4v8YTyvoSbgwLocecgQ=; b=eKF7T2h7MVNM twL9tlCWCR4a4OM9+ObvUhbdM5IIRvpNl2URKHuj59nTr64wKbo7tBo5QFi3otKR 9DnnaDB5Ey+zp5I2XOvmhQzqnaztW79yd/1OvLJGPtNnkPDO9ygA7x9EaMWdRHdp f7A7rBI6IymY8bIIpwwfsNO5OgtUVgg= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id EB5193002B3 for <57341@debbugs.gnu.org>; Mon, 22 Aug 2022 14:15:00 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.12; Mon, 22 Aug 2022 14:14:57 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 22 Aug 2022 14:14:41 +0200 Message-ID: <20220822121441.2235-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.2 In-Reply-To: <20220822121441.2235-1-madalinionel.patrascu@mdc-berlin.de> References: <20220822121441.2235-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-AS-Result: No-10--4.525000-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEAnn j551+g7jRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRvv4Y1Mygj09UP1 vHqmrVgTA9vLfVuC88oHQRlmHVYnGuz5caCZL4khOzgBH9wRPMo5A6wTicMJ0YDnmdMm9y0eYDT IhMw3OOX0tCKdnhB58I/9UW5M5dRMpg5yOcdoVgvcUt5lc1lLgKIzdZS3ou0Upb98rE4E6o8wNK hq0tvnN6saEKN1HiGr19ug4e2DhKhHW2rvirzDiRSooK5qU9MCQ5hwtR09izwQMfE+LreNKbQ+I wGNbxZ9ZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.525000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-SNTS-SMTP: 818B7D4BD5ECB4C4101DE5FF8D3E1FAB8BF58E9770D617EB09455BF4E3DD33132002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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")