diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..c94dda7 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^cache$ +^LICENSE\.md$ diff --git a/.gitignore b/.gitignore index b49a22a..9180b12 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ -/cache \ No newline at end of file +/cache +.Rproj.user diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..b1c2cf3 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,26 @@ +Package: tpeold +Title: Interface for Finding TPE-OLD Candidates +Version: 0.0.0.9000 +Authors@R: + person( + "Elias", + "Projahn", + email = "elias@johrpan.de", + role = c("aut", "cre") + ) +Description: This package provides a Shiny interface for analyzing genes and + finding TPE-OLD candidates based on known TPE-OLD genes. +License: AGPL (>= 3) +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.1.2 +Imports: + data.table, + DT, + geposan, + gprofiler2, + plotly, + rlang, + rclipboard, + shiny, + shinyjs diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..fab6548 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,659 @@ +GNU Affero General Public License +================================= + +_Version 3, 19 November 2007_ +_Copyright (C) 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains +free software for all its users. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + +Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + +A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + +The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + +An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing +under this license. + +The precise terms and conditions for copying, distribution and +modification follow. + +## TERMS AND CONDITIONS + +### 0. Definitions. + +"This License" refers to version 3 of the GNU Affero General Public +License. + +"Copyright" also means copyright-like laws that apply to other kinds +of works, such as semiconductor masks. + +"The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + +To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of +an exact copy. The resulting work is called a "modified version" of +the earlier work or a work "based on" the earlier work. + +A "covered work" means either the unmodified Program or a work based +on the Program. + +To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + +To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user +through a computer network, with no transfer of a copy, is not +conveying. + +An interactive user interface displays "Appropriate Legal Notices" to +the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + +### 1. Source Code. + +The "source code" for a work means the preferred form of the work for +making modifications to it. "Object code" means any non-source form of +a work. + +A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + +The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + +The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + +The Corresponding Source need not include anything that users can +regenerate automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same +work. + +### 2. Basic Permissions. + +All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, +without conditions so long as your license otherwise remains in force. +You may convey covered works to others for the sole purpose of having +them make modifications exclusively for you, or provide you with +facilities for running those works, provided that you comply with the +terms of this License in conveying all material for which you do not +control copyright. Those thus making or running the covered works for +you must do so exclusively on your behalf, under your direction and +control, on terms that prohibit them from making any copies of your +copyrighted material outside their relationship with you. + +Conveying under any other circumstances is permitted solely under the +conditions stated below. Sublicensing is not allowed; section 10 makes +it unnecessary. + +### 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such +circumvention is effected by exercising rights under this License with +respect to the covered work, and you disclaim any intention to limit +operation or modification of the work as a means of enforcing, against +the work's users, your or third parties' legal rights to forbid +circumvention of technological measures. + +### 4. Conveying Verbatim Copies. + +You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + +You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + +### 5. Conveying Modified Source Versions. + +You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these +conditions: + +- a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. +- b) The work must carry prominent notices stating that it is + released under this License and any conditions added under + section 7. This requirement modifies the requirement in section 4 + to "keep intact all notices". +- c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. +- d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + +A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + +### 6. Conveying Non-Source Forms. + +You may convey a covered work in object code form under the terms of +sections 4 and 5, provided that you also convey the machine-readable +Corresponding Source under the terms of this License, in one of these +ways: + +- a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. +- b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the Corresponding + Source from a network server at no charge. +- c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. +- d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. +- e) Convey the object code using peer-to-peer transmission, + provided you inform other peers where the object code and + Corresponding Source of the work are being offered to the general + public at no charge under subsection 6d. + +A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + +A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, +family, or household purposes, or (2) anything designed or sold for +incorporation into a dwelling. In determining whether a product is a +consumer product, doubtful cases shall be resolved in favor of +coverage. For a particular product received by a particular user, +"normally used" refers to a typical or common use of that class of +product, regardless of the status of the particular user or of the way +in which the particular user actually uses, or expects or is expected +to use, the product. A product is a consumer product regardless of +whether the product has substantial commercial, industrial or +non-consumer uses, unless such uses represent the only significant +mode of use of the product. + +"Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to +install and execute modified versions of a covered work in that User +Product from a modified version of its Corresponding Source. The +information must suffice to ensure that the continued functioning of +the modified object code is in no case prevented or interfered with +solely because modification has been made. + +If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + +The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or +updates for a work that has been modified or installed by the +recipient, or for the User Product in which it has been modified or +installed. Access to a network may be denied when the modification +itself materially and adversely affects the operation of the network +or violates the rules and protocols for communication across the +network. + +Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + +### 7. Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders +of that material) supplement the terms of this License with terms: + +- a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or +- b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or +- c) Prohibiting misrepresentation of the origin of that material, + or requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or +- d) Limiting the use for publicity purposes of names of licensors + or authors of the material; or +- e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or +- f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions + of it) with contractual assumptions of liability to the recipient, + for any liability that these contractual assumptions directly + impose on those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; the +above requirements apply either way. + +### 8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your license +from a particular copyright holder is reinstated (a) provisionally, +unless and until the copyright holder explicitly and finally +terminates your license, and (b) permanently, if the copyright holder +fails to notify you of the violation by some reasonable means prior to +60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run +a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + +An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +### 11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims owned +or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on +the non-exercise of one or more of the rights that are specifically +granted under this License. You may not convey a covered work if you +are a party to an arrangement with a third party that is in the +business of distributing software, under which you make payment to the +third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties +who would receive the covered work from you, a discriminatory patent +license (a) in connection with copies of the covered work conveyed by +you (or copies made from those copies), or (b) primarily for and in +connection with specific products or compilations that contain the +covered work, unless you entered into that arrangement, or that patent +license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under +this License and any other pertinent obligations, then as a +consequence you may not convey it at all. For example, if you agree to +terms that obligate you to collect a royalty for further conveying +from those to whom you convey the Program, the only way you could +satisfy both those terms and this License would be to refrain entirely +from conveying the Program. + +### 13. Remote Network Interaction; Use with the GNU General Public License. + +Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your +version supports such interaction) an opportunity to receive the +Corresponding Source of your version by providing access to the +Corresponding Source from a network server at no charge, through some +standard or customary means of facilitating copying of software. This +Corresponding Source shall include the Corresponding Source for any +work covered by version 3 of the GNU General Public License that is +incorporated pursuant to the following paragraph. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + +### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions +of the GNU Affero General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever +published by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future versions +of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +### 15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT +WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND +PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively state +the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as + published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper +mail. + +If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for +the specific requirements. + +You should also get your employer (if you work as a programmer) or +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. For more information on this, and how to apply and follow +the GNU AGPL, see . diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..20fc17a --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,5 @@ +# Generated by roxygen2: do not edit by hand + +export(run_app) +import(data.table) +import(shiny) diff --git a/R/app.R b/R/app.R new file mode 100644 index 0000000..554732e --- /dev/null +++ b/R/app.R @@ -0,0 +1,8 @@ +#' Run the application server. +#' +#' @param port The port to serve the application on. +#' +#' @export +run_app <- function(port = 3464) { + shiny::runApp(shiny::shinyApp(ui, server), port = port) +} diff --git a/data.R b/R/data.R similarity index 76% rename from data.R rename to R/data.R index 71ecb11..b90a385 100644 --- a/data.R +++ b/R/data.R @@ -1,6 +1,4 @@ -library(data.table) - -#' Species IDs of known replicatively aging species. +# Species IDs of known replicatively aging species. species_ids_replicative <- c( "bihybrid", "btaurus", @@ -29,14 +27,14 @@ species_ids_replicative <- c( "tgelada" ) -#' Species from [geposan] and their aging status. +# Species from [geposan] and their aging status. species <- geposan::species[, .( id, name, replicative = id %chin% species_ids_replicative )] -#' Gene names of genes for verified TPE-OLD genes. +# Gene names of genes for verified TPE-OLD genes. genes_verified_tpe_old <- c( "C1S", "DSP", @@ -45,7 +43,7 @@ genes_verified_tpe_old <- c( "TERT" ) -#' Gene names of genes with a suggested TPE-OLD. +# Gene names of genes with a suggested TPE-OLD. genes_suggested_tpe_old <- c( "AKAP3", "ANO2", @@ -60,7 +58,7 @@ genes_suggested_tpe_old <- c( "TSPAN9" ) -#' Genes from [geposan] and their TPE-OLD status. +# Genes from [geposan] and their TPE-OLD status. genes <- geposan::genes[, .( id, name, @@ -69,7 +67,7 @@ genes <- geposan::genes[, .( verified = name %chin% genes_verified_tpe_old )] -#' All available methods from [geposan] and additional information on them. +# All available methods from [geposan] and additional information on them. methods <- list( list( id = "clusteriness", @@ -93,10 +91,10 @@ methods <- list( ) ) -#' Gene IDs of known or suggested TPE-OLD genes. +# Gene IDs of known or suggested TPE-OLD genes. genes_tpe_old <- genes[suggested | verified == TRUE, id] -#' Preset for [geposan] including all species and TPE-OLD genes for reference. +# Preset for [geposan] including all species and TPE-OLD genes for reference. preset_all_species <- geposan::preset( methods = c("clusteriness", "correlation", "proximity", "neural"), species = species$id, @@ -104,8 +102,8 @@ preset_all_species <- geposan::preset( reference_genes = genes_tpe_old ) -#' Preset for [geposan] including only replicatively aging species as well as -#' TPE-OLD genes for reference. +# Preset for [geposan] including only replicatively aging species as well as +# TPE-OLD genes for reference. preset_replicative_species <- geposan::preset( methods = c("clusteriness", "correlation", "proximity", "neural"), species = species_ids_replicative, diff --git a/methods.R b/R/methods.R similarity index 91% rename from methods.R rename to R/methods.R index 6e64db1..e14db7b 100644 --- a/methods.R +++ b/R/methods.R @@ -1,6 +1,4 @@ -library(shiny) - -#' Construct UI for the methods editor. +# Construct UI for the methods editor. methods_ui <- function(id) { initial_weight <- 100 / length(methods) @@ -36,11 +34,11 @@ methods_ui <- function(id) { ) } -#' Construct server for the methods editor. -#' -#' @param analysis The reactive containing the results to be weighted. -#' -#' @return A reactive containing the weighted results. +# Construct server for the methods editor. +# +# @param analysis The reactive containing the results to be weighted. +# +# @return A reactive containing the weighted results. methods_server <- function(id, analysis) { moduleServer(id, function(input, output, session) { observeEvent(input$optimize_button, { diff --git a/rank_plot.R b/R/rank_plot.R similarity index 62% rename from rank_plot.R rename to R/rank_plot.R index 22a29e0..30bdbb9 100644 --- a/rank_plot.R +++ b/R/rank_plot.R @@ -1,23 +1,20 @@ -library(data.table) -library(plotly) - -#' Draw a plot displaying the rank of reference genes. -#' -#' The input table should contain the following columns: -#' -#' - `gene` Gene IDs of genes to display. -#' - `name` Name of genes to display. -#' - `score` Score of the genes. -#' - `rank` Rank of the genes based on the score. -#' -#' @param results Results to display. -#' @param reference_gene_ids IDs of reference genes. -#' @param cutoff Cut-off score. +# Draw a plot displaying the rank of reference genes. +# +# The input table should contain the following columns: +# +# - `gene` Gene IDs of genes to display. +# - `name` Name of genes to display. +# - `score` Score of the genes. +# - `rank` Rank of the genes based on the score. +# +# @param results Results to display. +# @param reference_gene_ids IDs of reference genes. +# @param cutoff Cut-off score. rank_plot <- function(results, reference_gene_ids, cutoff) { first_not_included_rank <- results[score < cutoff, min(rank)] last_rank <- results[, .N] - plot <- plot_ly() |> add_trace( + plot <- plotly::plot_ly() |> plotly::add_trace( data = results, x = ~rank, y = ~score, @@ -25,7 +22,7 @@ rank_plot <- function(results, reference_gene_ids, cutoff) { type = "scatter", mode = "line", hoverinfo = "skip" - ) |> add_trace( + ) |> plotly::add_trace( data = results[gene %chin% reference_gene_ids], x = ~rank, y = ~score, @@ -33,13 +30,13 @@ rank_plot <- function(results, reference_gene_ids, cutoff) { name = ~name, width = 10, type = "bar" - ) |> layout( + ) |> plotly::layout( xaxis = list(title = "Ranks"), yaxis = list(title = "Score") ) if (first_not_included_rank <= last_rank) { - plot <- plot |> layout( + plot <- plot |> plotly::layout( shapes = list( type = "rect", fillcolor = "black", diff --git a/scatter_plot.R b/R/scatter_plot.R similarity index 56% rename from scatter_plot.R rename to R/scatter_plot.R index 3c1aecd..f10b13d 100644 --- a/scatter_plot.R +++ b/R/scatter_plot.R @@ -1,24 +1,20 @@ -library(data.table) -library(plotly) - -#' Draw a scatter plot containing gene positions. -#' -#' @param results Results from [`process_input()`]. -#' @param species Species to be displayed. -#' @param genes Genes to be displayed. -#' @param distances Distance data to display. -scatter_plot <- function(results, species, genes, distances) { +# Draw a scatter plot containing gene positions. +# +# @param results Results from [`process_input()`]. +# @param species Species to be displayed. +# @param genes Genes to be displayed. +scatter_plot <- function(results, species, genes) { species_ids <- species[, id] data <- merge( genes[, .(id, name)], - distances[species %in% species_ids], + geposan::distances[species %in% species_ids], by.x = "id", by.y = "gene" ) data[name == "", name := "Unknown"] - plot_ly( + plotly::plot_ly( data = data, x = ~species, y = ~distance, @@ -26,7 +22,7 @@ scatter_plot <- function(results, species, genes, distances) { name = ~name, type = "scatter", mode = "markers" - ) |> layout( + ) |> plotly::layout( xaxis = list( title = "Species", tickvals = species_ids, @@ -34,4 +30,4 @@ scatter_plot <- function(results, species, genes, distances) { ), yaxis = list(title = "Distance to telomeres [Bp]") ) -} \ No newline at end of file +} diff --git a/server.R b/R/server.R similarity index 83% rename from server.R rename to R/server.R index 55bf97b..44df265 100644 --- a/server.R +++ b/R/server.R @@ -1,18 +1,5 @@ -library(data.table) -library(DT) -library(geposan) -library(gprofiler2) -library(plotly) -library(rclipboard) -library(shiny) - -source("methods.R") -source("rank_plot.R") -source("scatter_plot.R") -source("utils.R") - -#' Java script function to replace gene IDs with Ensembl gene links. -js_link <- JS("function(row, data) { +# Java script function to replace gene IDs with Ensembl gene links. +js_link <- DT::JS("function(row, data) { let id = data[1]; var name = data[2]; if (!name) name = 'Unknown'; @@ -21,7 +8,7 @@ js_link <- JS("function(row, data) { }") server <- function(input, output, session) { - #' Show the customized slider for setting the required number of species. + # Show the customized slider for setting the required number of species. output$n_species_slider <- renderUI({ sliderInput( "n_species", @@ -37,7 +24,7 @@ server <- function(input, output, session) { ) }) - #' Compute the results according to the preset. + # Compute the results according to the preset. analysis <- reactive({ # Select the preset. preset <- if (input$species == "all") { @@ -70,7 +57,7 @@ server <- function(input, output, session) { ) # Count included species from the preset per gene. - genes_n_species <- distances[ + genes_n_species <- geposan::distances[ species %chin% preset$species_ids, .(n_species = .N), by = "gene" @@ -85,18 +72,18 @@ server <- function(input, output, session) { # Rank the results. results <- methods_server("methods", analysis) - #' Apply the cut-off score to the ranked results. + # Apply the cut-off score to the ranked results. results_filtered <- reactive({ results()[score >= input$cutoff / 100] }) - output$genes <- renderDT({ + output$genes <- DT::renderDT({ method_ids <- sapply(methods, function(method) method$id) method_names <- sapply(methods, function(method) method$name) columns <- c("rank", "gene", "name", "chromosome", method_ids, "score") column_names <- c("", "Gene", "", "Chromosome", method_names, "Score") - dt <- datatable( + dt <- DT::datatable( results_filtered()[, ..columns], rownames = FALSE, colnames = column_names, @@ -112,7 +99,7 @@ server <- function(input, output, session) { ) ) - formatPercentage(dt, c(method_ids, "score"), digits = 1) + DT::formatPercentage(dt, c(method_ids, "score"), digits = 1) }) output$copy <- renderUI({ @@ -126,13 +113,13 @@ server <- function(input, output, session) { splitLayout( cellWidths = "auto", - rclipButton( + rclipboard::rclipButton( "copy_ids_button", "Copy gene IDs", genes_text, icon = icon("clipboard") ), - rclipButton( + rclipboard::rclipButton( "copy_names_button", "Copy gene names", names_text, @@ -141,7 +128,7 @@ server <- function(input, output, session) { ) }) - output$scatter <- renderPlotly({ + output$scatter <- plotly::renderPlotly({ results <- results_filtered() gene_ids <- results[input$genes_rows_selected, gene] @@ -153,7 +140,7 @@ server <- function(input, output, session) { species[replicative == TRUE] } - scatter_plot(results, species, genes, distances) + scatter_plot(results, species, genes) }) output$assessment_synopsis <- renderText({ @@ -190,7 +177,7 @@ server <- function(input, output, session) { ) }) - output$rank_plot <- renderPlotly({ + output$rank_plot <- plotly::renderPlotly({ rank_plot( results(), genes[suggested | verified == TRUE, id], @@ -198,10 +185,18 @@ server <- function(input, output, session) { ) }) - output$gost <- renderPlotly({ + output$gost <- plotly::renderPlotly({ if (input$enable_gost) { - result <- gost(results_filtered()[, gene], ordered_query = TRUE) - gostplot(result, capped = FALSE, interactive = TRUE) + result <- gprofiler2::gost( + results_filtered()[, gene], + ordered_query = TRUE + ) + + gprofiler2::gostplot( + result, + capped = FALSE, + interactive = TRUE + ) } else { NULL } diff --git a/ui.R b/R/ui.R similarity index 89% rename from ui.R rename to R/ui.R index d734d86..7625193 100644 --- a/ui.R +++ b/R/ui.R @@ -1,13 +1,6 @@ -library(DT) -library(plotly) -library(rclipboard) -library(shiny) - -source("methods.R") - ui <- fluidPage( shinyjs::useShinyjs(), - rclipboardSetup(), + rclipboard::rclipboardSetup(), titlePanel("TPE-OLD candidates"), sidebarLayout( sidebarPanel( @@ -42,12 +35,12 @@ ui <- fluidPage( uiOutput("copy"), div( style = "margin-top: 16px", - DTOutput("genes", height = "1000px") + DT::DTOutput("genes", height = "1000px") ) ), tabPanel( "Positions", - plotlyOutput( + plotly::plotlyOutput( "scatter", width = "100%", height = "600px" @@ -58,7 +51,7 @@ ui <- fluidPage( htmlOutput("assessment_synopsis"), div( style = "margin-top: 16px", - plotlyOutput( + plotly::plotlyOutput( "rank_plot", width = "100%", height = "600px" @@ -74,7 +67,7 @@ ui <- fluidPage( ), conditionalPanel( "input.enable_gost == true", - plotlyOutput( + plotly::plotlyOutput( "gost", width = "100%", height = "600px" diff --git a/utils.R b/R/utils.R similarity index 59% rename from utils.R rename to R/utils.R index 94b56db..a373fac 100644 --- a/utils.R +++ b/R/utils.R @@ -1,10 +1,8 @@ -library(rlog) - -#' Run a function caching the result on the file system. -#' -#' The function will be called with the appended arguments. The [`id`] argument -#' will be used to identify the cache file on the file system and in log -#' messages. +# Run a function caching the result on the file system. +# +# The function will be called with the appended arguments. The [`id`] argument +# will be used to identify the cache file on the file system and in log +# messages. run_cached <- function(id, func, ...) { if (!dir.exists("cache")) { dir.create("cache") @@ -13,8 +11,6 @@ run_cached <- function(id, func, ...) { cache_file <- paste("cache/", id, ".rds", sep = "") if (file.exists(cache_file)) { - log_info(sprintf("Loading %s from cache", id)) - # If the cache file exists, we restore the data from it. readRDS(cache_file) } else { @@ -27,3 +23,9 @@ run_cached <- function(id, func, ...) { data } } + +# This is needed to make data.table's and shiny's symbols available within the +# package. +#' @import data.table +#' @import shiny +NULL diff --git a/main.R b/main.R deleted file mode 100644 index 9e01819..0000000 --- a/main.R +++ /dev/null @@ -1,9 +0,0 @@ -library(shiny) - -# Initialize data first. -source("data.R") - -source("server.R") -source("ui.R") - -runApp(shinyApp(ui, server)) diff --git a/man/run_app.Rd b/man/run_app.Rd new file mode 100644 index 0000000..c408207 --- /dev/null +++ b/man/run_app.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/app.R +\name{run_app} +\alias{run_app} +\title{Run the application server.} +\usage{ +run_app(port = 3464) +} +\arguments{ +\item{port}{The port to serve the application on.} +} +\description{ +Run the application server. +}