From unknown Sun Jun 22 08:03:43 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#66913] [PATCH] gnu: Add r-miamiplot. Resent-From: "Afkhami, Navid" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Nov 2023 13:07:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 66913 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66913@debbugs.gnu.org Cc: "Afkhami, Navid" X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16990168026536 (code B ref -1); Fri, 03 Nov 2023 13:07:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Nov 2023 13:06:42 +0000 Received: from localhost ([127.0.0.1]:57274 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytsn-0001hL-AU for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:06:42 -0400 Received: from lists.gnu.org ([2001:470:142::17]:35344) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytsg-0001h0-Oj for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:06:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qyts1-0001IC-00 for guix-patches@gnu.org; Fri, 03 Nov 2023 09:05:53 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qytrn-0005Hj-NE for guix-patches@gnu.org; Fri, 03 Nov 2023 09:05:50 -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=1699016734; x=1700831135; bh=nDfXjagchlFmvUe 4VWhIOQgkYY+HlimJNkt2V5cUKGo=; b=T/m2v9yUMU8vdgE+4bQtNOS/wYkAtBo pBkQzJnmTkC3EJ8OCE+ub7PdDL6jmygkCvgg4fxs9Tlw8g6v5bIb0QOD9YgZp8pH XxsV/zxvdRJXXNBMcECmZ0dDDOdWg8qN5hE+vHH92tiUX++G/EDtaJty6WKrNg0P BTERLLfo5fnk= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id CB6AB1601B5 for ; Fri, 3 Nov 2023 14:05:34 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 3 Nov 2023 14:05:34 +0100 From: "Afkhami, Navid" Date: Fri, 3 Nov 2023 13:05:29 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-AS-Result: No-10--7.071400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6V6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/RfJTOWMuxOdsV8o+pqqC6AlEwlpQS2lgULGoTjCGdeUL//VMxXlyE8gVyTd/p+/ITDY 4dCWoPQJwyxC8d/tsm3mxErTrAdXhZvxJrutTlmoX6pCkJZNSOSbH0QLHlTYFD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58I/9UW5M5dRPPo+3Q0H/f/uloYgzjonrsymsk/wUE4hofJD4mIZwnTD1nO YpEsUfnj0AP9fQBhdaf7cWuH6e3us6XN7NbmTE5 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.071400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-SNTS-SMTP: 9EF8AA73E4AECEDD7F19967606F5861E8C836AE26DE4E95B239555CB4EA96CA52000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (r-miamiplot): New variable. Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06 --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a4bcd093a..e36593fd8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10665,6 +10665,40 @@ (define-public r-scde ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-miamiplot + (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0") + (revision "1")) + (package + (name "r-miamiplot") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/juliedwhite/miamiplot") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9")))) + (properties `((upstream-name . "miamiplot"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-magrittr + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/juliedwhite/miamiplot") + (synopsis "Create a ggplot2 miami plot") + (description + "This package generates a Miami plot with centered chromosome labels. +The output is a ggplot2 object. Users can specify which data they +want plotted on top vs. bottom , whether to display significance +line(s), what colors to give chromosomes, and what points to label.") + (license license:gpl2)))) + (define-public r-millefy (package (name "r-millefy") base-commit: 28ebbe2be8829a4767b9789c6353ad5e826d1164 -- 2.34.1 From unknown Sun Jun 22 08:03:43 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: "Afkhami, Navid" Subject: bug#66913: closed ([PATCH] gnu: Add r-miamiplot.) Message-ID: References: <87zfzvrnh5.fsf@elephly.net> X-Gnu-PR-Message: they-closed 66913 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 66913@debbugs.gnu.org Date: Fri, 03 Nov 2023 13:12:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1699017122-7017-1" This is a multi-part message in MIME format... ------------=_1699017122-7017-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #66913: [PATCH] gnu: Add r-miamiplot. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 66913@debbugs.gnu.org. --=20 66913: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D66913 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1699017122-7017-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 66913-done) by debbugs.gnu.org; 3 Nov 2023 13:11:47 +0000 Received: from localhost ([127.0.0.1]:57279 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytxi-0001ok-UR for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:11:47 -0400 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21852) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytxh-0001oc-DF for 66913-done@debbugs.gnu.org; Fri, 03 Nov 2023 09:11:46 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1699017066; cv=none; d=zohomail.com; s=zohoarc; b=XLxlu95TksJCHMXtJKhRah/CLCbmcw9ITkSl+VtH0r2vAd4OvnMQoMe4ZkhPZDYNWM7MsRwT67bUkfKQUv3vnjd5LCDal3RtVMVA4Im5wGJc1+qnJB5KRCm4Tel5eQx3L4Pvhqz3wRE5QqVOm+1qmwWeTnu479rKmc/sc9Fm1Dc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1699017066; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=DsBMjktYxkI727XZHJAqrSBURNFhaXeeka7nTb/NqUr7rxY/Vb2ka8pqRmoMP71AZ3sNh28EIqWjLlI0ks6YhT2i/3r3JRCXfy8kGl0Y29lnCrNfvHx5r43ZF7d0PDIrrJMaTBxRSq0iVaNWHTvV92g1Dieu/Opx0+UMAcMxMPI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1699017066; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=Dfq5vU2nI9cu2Qv2WfXwCimUsmSPSRb19Yl2OFYifgXsU1mGd3OUcVuBZc8kFb47 /A8RBR7FCxGDOZM3X6cnhRE9XQ3hTPtxPydlJmhdDkLoth1FAMnd4KxhWN8VGXv4Loq kElPm9e+guyf2lxRIofS10nTC8NTk0F36oxrzYH8= Received: from localhost (215-110-142-46.pool.kielnet.net [46.142.110.215]) by mx.zohomail.com with SMTPS id 1699017065277447.0343167621511; Fri, 3 Nov 2023 06:11:05 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: 66913-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-miamiplot. Date: Fri, 03 Nov 2023 14:10:42 +0100 Message-ID: <87zfzvrnh5.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66913-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Applied, thank you! -- Ricardo ------------=_1699017122-7017-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Nov 2023 13:06:42 +0000 Received: from localhost ([127.0.0.1]:57274 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytsn-0001hL-AU for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:06:42 -0400 Received: from lists.gnu.org ([2001:470:142::17]:35344) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qytsg-0001h0-Oj for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:06:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qyts1-0001IC-00 for guix-patches@gnu.org; Fri, 03 Nov 2023 09:05:53 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qytrn-0005Hj-NE for guix-patches@gnu.org; Fri, 03 Nov 2023 09:05:50 -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=1699016734; x=1700831135; bh=nDfXjagchlFmvUe 4VWhIOQgkYY+HlimJNkt2V5cUKGo=; b=T/m2v9yUMU8vdgE+4bQtNOS/wYkAtBo pBkQzJnmTkC3EJ8OCE+ub7PdDL6jmygkCvgg4fxs9Tlw8g6v5bIb0QOD9YgZp8pH XxsV/zxvdRJXXNBMcECmZ0dDDOdWg8qN5hE+vHH92tiUX++G/EDtaJty6WKrNg0P BTERLLfo5fnk= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id CB6AB1601B5 for ; Fri, 3 Nov 2023 14:05:34 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 3 Nov 2023 14:05:34 +0100 From: "Afkhami, Navid" To: Subject: [PATCH] gnu: Add r-miamiplot. Date: Fri, 3 Nov 2023 13:05:29 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-AS-Result: No-10--7.071400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6V6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/RfJTOWMuxOdsV8o+pqqC6AlEwlpQS2lgULGoTjCGdeUL//VMxXlyE8gVyTd/p+/ITDY 4dCWoPQJwyxC8d/tsm3mxErTrAdXhZvxJrutTlmoX6pCkJZNSOSbH0QLHlTYFD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58I/9UW5M5dRPPo+3Q0H/f/uloYgzjonrsymsk/wUE4hofJD4mIZwnTD1nO YpEsUfnj0AP9fQBhdaf7cWuH6e3us6XN7NbmTE5 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.071400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-SNTS-SMTP: 9EF8AA73E4AECEDD7F19967606F5861E8C836AE26DE4E95B239555CB4EA96CA52000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: submit Cc: "Afkhami, Navid" X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (r-miamiplot): New variable. Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06 --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a4bcd093a..e36593fd8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10665,6 +10665,40 @@ (define-public r-scde ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-miamiplot + (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0") + (revision "1")) + (package + (name "r-miamiplot") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/juliedwhite/miamiplot") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9")))) + (properties `((upstream-name . "miamiplot"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-magrittr + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/juliedwhite/miamiplot") + (synopsis "Create a ggplot2 miami plot") + (description + "This package generates a Miami plot with centered chromosome labels. +The output is a ggplot2 object. Users can specify which data they +want plotted on top vs. bottom , whether to display significance +line(s), what colors to give chromosomes, and what points to label.") + (license license:gpl2)))) + (define-public r-millefy (package (name "r-millefy") base-commit: 28ebbe2be8829a4767b9789c6353ad5e826d1164 -- 2.34.1 ------------=_1699017122-7017-1--