diff --git a/DESCRIPTION b/DESCRIPTION
index a293f5c5..e7bfe5d8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,8 @@ Imports:
dplyr,
tidyselect,
gplots,
- ggplot2
+ ggplot2,
+ rlang
Suggests:
BiocManager,
knitr,
@@ -39,6 +40,7 @@ Depends:
URL: https://um-applied-algorithms-lab.github.io/PTMsToPathways/
BugReports: https://github.com/UM-Applied-Algorithms-Lab/PTMsToPathways/issues/new
LazyData: true
+LazyDataCompression: xz
Config/testthat/edition: 3
Additional_repositories: https://bioconductor.org/packages/3.21/bioc
biocViews: Software, Proteomics, PostTranslationalModifications, Pathways, Network
diff --git a/LICENSE.md b/LICENSE.md
deleted file mode 100644
index 175443ce..00000000
--- a/LICENSE.md
+++ /dev/null
@@ -1,595 +0,0 @@
-GNU General Public License
-==========================
-
-_Version 3, 29 June 2007_
-_Copyright © 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 General Public License is a free, copyleft license for software and other
-kinds of works.
-
-The licenses for most software and other practical works are designed to take away
-your freedom to share and change the works. By contrast, the GNU General Public
-License is 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. We, the Free
-Software Foundation, use the GNU General Public License for most of our software; it
-applies also to any other work released this way by its authors. You can apply it to
-your programs, too.
-
-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.
-
-To protect your rights, we need to prevent others from denying you these rights or
-asking you to surrender the rights. Therefore, you have certain responsibilities if
-you distribute copies of the software, or if you modify it: responsibilities to
-respect the freedom of others.
-
-For example, if you distribute copies of such a program, whether gratis or for a fee,
-you must pass on to the recipients the same freedoms that you received. You must make
-sure that they, too, receive or can get the source code. And you must show them these
-terms so they know their rights.
-
-Developers that use the GNU GPL protect your rights with two steps: **(1)** assert
-copyright on the software, and **(2)** offer you this License giving you legal permission
-to copy, distribute and/or modify it.
-
-For the developers' and authors' protection, the GPL clearly explains that there is
-no warranty for this free software. For both users' and authors' sake, the GPL
-requires that modified versions be marked as changed, so that their problems will not
-be attributed erroneously to authors of previous versions.
-
-Some devices are designed to deny users access to install or run modified versions of
-the software inside them, although the manufacturer can do so. This is fundamentally
-incompatible with the aim of protecting users' freedom to change the software. The
-systematic pattern of such abuse occurs in the area of products for individuals to
-use, which is precisely where it is most unacceptable. Therefore, we have designed
-this version of the GPL to prohibit the practice for those products. If such problems
-arise substantially in other domains, we stand ready to extend this provision to
-those domains in future versions of the GPL, as needed to protect the freedom of
-users.
-
-Finally, every program is threatened constantly by software patents. States should
-not allow patents to restrict development and use of software on general-purpose
-computers, but in those that do, we wish to avoid the special danger that patents
-applied to a free program could make it effectively proprietary. To prevent this, the
-GPL assures that patents cannot be used to render the program non-free.
-
-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 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. Use with the GNU Affero General Public License
-
-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 Affero
-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 special requirements of the GNU Affero General Public License, section
-13, concerning interaction through a network will apply to the combination as such.
-
-### 14. Revised Versions of this License
-
-The Free Software Foundation may publish revised and/or new versions of the GNU
-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 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
-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
-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 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 General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program does terminal interaction, make it output a short notice like this
-when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type 'show c' for details.
-
-The hypothetical commands `show w` and `show c` should show the appropriate parts of
-the General Public License. Of course, your program's commands might be different;
-for a GUI interface, you would use an “about box”.
-
-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 GPL, see
-<>.
-
-The GNU General Public License does not permit incorporating your program into
-proprietary programs. If your program is a subroutine library, you may consider it
-more useful to permit linking proprietary applications with the library. If this is
-what you want to do, use the GNU Lesser General Public License instead of this
-License. But first, please read
-<>.
diff --git a/NAMESPACE b/NAMESPACE
index 58ba02f6..318aedec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -43,3 +43,4 @@ export(strip.cy.goo)
importFrom(gplots,heatmap.2)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl)
+importFrom(rlang,.data)
diff --git a/R/BRCAHelpers.R b/R/BRCAHelpers.R
index d9fc7023..5c5e5c2d 100644
--- a/R/BRCAHelpers.R
+++ b/R/BRCAHelpers.R
@@ -88,7 +88,7 @@ graph.ptm.by.cluster <- function(
safe_dist2 <- function(m, min.shared = 2) {
m <- as.matrix(m)
nr <- nrow(m)
- if (nr <= 1) return(as.dist(matrix(0, nr, nr)))
+ if (nr <= 1) return(stats::as.dist(matrix(0, nr, nr)))
dmat <- matrix(0, nr, nr)
rownames(dmat) <- colnames(dmat) <- rownames(m)
for (i in seq_len(nr - 1)) {
@@ -102,14 +102,14 @@ graph.ptm.by.cluster <- function(
fallback <- if (length(fv)) 2 * max(fv) else 1
dmat[!is.finite(dmat)] <- fallback
diag(dmat) <- 0
- as.dist(dmat)
+ stats::as.dist(dmat)
}
## row-wise linear slope helper for order.rows = "slope"
row_slope <- function(v) {
ok <- which(is.finite(v))
if (length(ok) < 2) return(NA_real_)
- coef(lm(v[ok] ~ ok))[2]
+ stats::coef(stats::lm(v[ok] ~ ok))[2]
}
## high-contrast qualitative palette for cluster sidebar
@@ -154,13 +154,13 @@ graph.ptm.by.cluster <- function(
write_cluster_legend <- function(cluster.palette, filename, cex = 0.9) {
n <- length(cluster.palette)
ncol <- if (n > 18) 2L else 1L
- pdf(filename,
+ grDevices::pdf(filename,
width = max(5, 3 * ncol),
height = max(4, 0.32 * ceiling(n / ncol) + 1))
- on.exit(dev.off())
- par(mar = c(0.3, 0.3, 0.3, 0.3), xpd = NA)
- plot.new()
- legend("topleft",
+ on.exit(grDevices::dev.off())
+ graphics::par(mar = c(0.3, 0.3, 0.3, 0.3), xpd = NA)
+ graphics::plot.new()
+ graphics::legend("topleft",
inset = 0.01,
legend = names(cluster.palette),
fill = cluster.palette,
@@ -180,16 +180,16 @@ graph.ptm.by.cluster <- function(
brks <- seq(-zlim, zlim, length.out = n + 1L)
z <- matrix(seq_len(n), nrow = 1L, ncol = n) # 1 x n
- pdf(filename, width = 1.8, height = 4.5)
- on.exit(dev.off())
+ grDevices::pdf(filename, width = 1.8, height = 4.5)
+ on.exit(grDevices::dev.off())
# left margin wide enough for the bar; right margin for axis labels
- par(mar = c(2, 1.0, 1.5, 2.8))
+ graphics::par(mar = c(2, 1.0, 1.5, 2.8))
# x: 2 breakpoints = 1 column; y: n+1 breakpoints = n rows
- image(x = c(0, 1), y = brks, z = z,
+ graphics::image(x = c(0, 1), y = brks, z = z,
col = cols, xaxt = "n", yaxt = "n", xlab = "", ylab = "")
- axis(4, at = pretty(c(-zlim, zlim)), las = 2, cex.axis = 0.85)
- mtext("Signal", side = 4, line = 1.8, cex = 0.85)
- box()
+ graphics::axis(4, at = pretty(c(-zlim, zlim)), las = 2, cex.axis = 0.85)
+ graphics::mtext("Signal", side = 4, line = 1.8, cex = 0.85)
+ graphics::box()
}
# ---- data prep -----------------------------------------------------
@@ -218,7 +218,7 @@ graph.ptm.by.cluster <- function(
mean = subm[order(rowMeans(subm, na.rm=TRUE), decreasing=TRUE, na.last=TRUE), , drop=FALSE],
slope = { sl <- apply(subm, 1, row_slope)
subm[order(sl, decreasing=TRUE, na.last=TRUE), , drop=FALSE] },
- hclust = subm[hclust(safe_dist2(subm, min.shared))$order, , drop=FALSE],
+ hclust = subm[stats::hclust(safe_dist2(subm, min.shared))$order, , drop=FALSE],
subm # "as.is"
)
}
@@ -232,7 +232,7 @@ graph.ptm.by.cluster <- function(
mat <- do.call(rbind, ordered.blocks)
if (cluster.cols && ncol(mat) > 1) {
- mat <- mat[, hclust(safe_dist2(t(mat), min.shared))$order, drop=FALSE]
+ mat <- mat[, stats::hclust(safe_dist2(t(mat), min.shared))$order, drop=FALSE]
}
cluster.sizes <- sapply(ordered.blocks, nrow)
@@ -257,7 +257,7 @@ graph.ptm.by.cluster <- function(
# ---- heatmap (key = FALSE → no internal key panel) ---------------
- pdf(filename, width = pdf.w, height = pdf.h)
+ grDevices::pdf(filename, width = pdf.w, height = pdf.h)
gplots::heatmap.2(
mat,
Rowv = FALSE,
@@ -285,7 +285,7 @@ graph.ptm.by.cluster <- function(
margins = c(10, 6),
main = main
)
- dev.off()
+ grDevices::dev.off()
message("Heatmap written to: ", filename)
# ---- optional legend files ----------------------------------------
diff --git a/R/BuildClusterFilteredNetwork.R b/R/BuildClusterFilteredNetwork.R
index ab4c4411..c7af98dc 100644
--- a/R/BuildClusterFilteredNetwork.R
+++ b/R/BuildClusterFilteredNetwork.R
@@ -18,7 +18,8 @@
#'
#' @export
#' @examples
-#' Example_Output <- BuildClusterFilteredNetwork(ex_gene_cccn_edges, ex_stringdb_edges, ex_genemania_edges)
+#' Example_Output <- BuildClusterFilteredNetwork(ex_gene_cccn_edges,
+#' ex_stringdb_edges, ex_genemania_edges)
#' utils::head(Example_Output[[2]])
BuildClusterFilteredNetwork <- function(gene.cccn.edges, stringdb.edges = NULL, genemania.edges = NULL, kinsub.edges = NULL, db.filepaths = c(NULL)) {
# Combine PPIs from different databases
diff --git a/R/CytoscapeGraphingFunctions.R b/R/CytoscapeGraphingFunctions.R
index 0630a731..50ab8db5 100644
--- a/R/CytoscapeGraphingFunctions.R
+++ b/R/CytoscapeGraphingFunctions.R
@@ -1,10 +1,7 @@
# @title Graphing and Manipulating Cluster Filtered Network
#
-# @description Creates a cytoscape graph of the cluster filtered network. Ensure that you have the Cytoscape app open and the RCy3 package downloaded.
-# The package RCy3 is required for many of the functions in this script. To download, run:
-# - if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
-# - BiocManager::install("RCy3")
-# It is also recommended (but not required) that users load RCy3 with library(RCy3) to access its functions directly.
+# @description Creates a cytoscape graph of the cluster filtered network. Ensure
+# that you have the Cytoscape app open and the RCy3 package downloaded.
#
# @details Graph Key
# - Node Size
@@ -312,7 +309,7 @@ strip.cy.goo <- function(test) {
#'
#' @return Called for its side effects; creates a network in Cytoscape.
#' @export
-cytoscape.graph.PCN.pathways <- function(PCN = pathway.crosstalk.network, net.name, Jaccard.edges=TRUE) {
+cytoscape.graph.PCN.pathways <- function(PCN, net.name, Jaccard.edges=TRUE) {
PCN.df <- data.frame(id=unique(c(PCN$source, PCN$target)))
if (Jaccard.edges== FALSE) {PCN = PCN[-which (PCN$interaction=="pathway Jaccard similarity"),]}
# Get rid of zero weight edges
@@ -352,7 +349,7 @@ make.gene.data.from.ptmtable <- function(genes, ptmtable) {
gene.data <- subset.ptmtable |>
dplyr::group_by(.data$Gene.Name) |>
dplyr::summarise(
- dplyr::across(where(is.numeric), ~sum(.x, na.rm = TRUE)),
+ dplyr::across(dplyr::where(is.numeric), ~sum(.x, na.rm = TRUE)),
.groups = "drop"
)
@@ -374,11 +371,13 @@ make.gene.data.from.ptmtable <- function(genes, ptmtable) {
#' summarised PTM values to the node table. Defaults to \code{FALSE}.
#' @param include.coclustered.PTMs Logical; if \code{TRUE}, add co-clustered
#' PTM nodes and their edges to the output. Defaults to \code{FALSE}.
+#' @param ptm.cccn.edges A data frame of PTM co-expression correlation network
+#' edges with PTM identifiers as node names, required if \code{include.coclustered.PTMs = TRUE}.
#'
#' @return A data frame of node attributes with an \code{id} column suitable
#' for \code{RCy3::createNetworkFromDataFrames}.
#' @export
-make.cytoscape.node.file <- function(edge.file, funckey, ptmtable, include.gene.data = FALSE, include.coclustered.PTMs = FALSE) {
+make.cytoscape.node.file <- function(edge.file, funckey = PTMsToPathways::function_key, ptmtable, include.gene.data = FALSE, include.coclustered.PTMs = FALSE, ptm.cccn.edges = NULL) {
# Step 1: get unique nodes from edge file
edge_nodes <- unique(c(as.character(edge.file[, 1]), as.character(edge.file[, 2])))
# check if there are PTMs in edgefile
@@ -416,7 +415,7 @@ make.cytoscape.node.file <- function(edge.file, funckey, ptmtable, include.gene.
node_file <- cbind(data.frame(id = node_file$Gene.Name), node_file)
# Step 4: Optionally merge PTM CCCN and data
if (include.coclustered.PTMs == TRUE) {
- edge.file.with.ptms <- get.co.clustered.ptms(edge.file, ptm.cccn.edges)
+ edge.file.with.ptms <- get.co.clustered.ptms(edge.file, ptm.cccn.edges, ptmtable)
if(length (peptides) > 0) {
edge.file.with.ptms <- unique(rbind(edge.file.with.ptms, edge.file[which(edge.file$interaction == "peptide"), ]))
}
@@ -470,11 +469,12 @@ make.genepep.edges <- function(peptide.edgefile) {
#' @param edge.file A data frame edge list whose nodes are gene names.
#' @param ptm.cccn.edges A data frame of PTM co-expression correlation network
#' edges with PTM identifiers as node names.
+#' @param ptmtable A PTM data frame with PTM identifiers as row names and numeric condition columns.
#'
#' @return An edge data frame combining the original gene edges, co-clustered
#' PTM edges, and gene-to-peptide linking edges.
#' @export
-get.co.clustered.ptms <- function (edge.file, ptm.cccn.edges) {
+get.co.clustered.ptms <- function (edge.file, ptm.cccn.edges, ptmtable) {
gene_nodes <- unique(c(as.character(edge.file[, 1]), as.character(edge.file[, 2])))
ptmtable.temp <- ptmtable
ptmtable.temp$Gene.Name <- sapply(rownames(ptmtable.temp), function (x) strsplit(x, " ", fixed = TRUE)[[1]][1])
@@ -572,7 +572,7 @@ harmonize_cfs <- function(edge.file.with.ptms, genecf, ptmtable) {
pepcf.funcs <- merge(
pepcf,
- funckey[, annotation_cols, drop = FALSE],
+ function_key[, annotation_cols, drop = FALSE],
by = "Gene.Name",
all.x = TRUE
)
@@ -658,6 +658,9 @@ mergeEdges <- function(edgefile) {
#'
#' @param ptms Character vector of PTM site strings (e.g., \"TP53 p S15\")
#' @param cfn List or data frame representing the cluster filtered network (default: global cfn.merged)
+#' @param ptm.cccn.edges A data frame of PTM co-expression correlation network
+#' edges with PTM identifiers as node names
+#' @param ptmtable A data frame containing PTM identifiers as row names and numeric condition columns
#' @param pepsep Character used to split ambiguous PTM entries (default: \";\")
#'
#' @return Subnetwork object with co-clustered PTMs and genes
@@ -673,10 +676,11 @@ mergeEdges <- function(edgefile) {
#' # Suppose filter.edges.0 and get.co.clustered.ptms are also defined and loaded
#' # The following returns the gene/PTM subnetwork
#' \dontrun{
-#' res <- ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";")
+#' res <- ptms_to_cfn(ptms, cfn = cfn.merged,
+#' ptm.cccn.edges = ptm.cccn.edges, ptmtable = ptmtable, pepsep = ";")
#' print(res)
#' }
-ptms_to_cfn <- function(ptms, cfn = cfn.merged, pepsep = ";") {
+ptms_to_cfn <- function(ptms, cfn, ptm.cccn.edges, ptmtable, pepsep = ";") {
ambig.ptms <- ptms[grep(";", ptms)]
if (length(ambig.ptms) > 0) {
@@ -697,8 +701,8 @@ ptms_to_cfn <- function(ptms, cfn = cfn.merged, pepsep = ";") {
all_genes <- unique(sapply(ptms, function (x) unlist(strsplit(x, " ", fixed=TRUE))[1]))
}
- sub.cfn <- filter.edges.0(all_genes, cfn.merged)
- sub.cfn.cccn <- get.co.clustered.ptms(sub.cfn, ptm.cccn.edges)
+ sub.cfn <- filter.edges.0(all_genes, cfn)
+ sub.cfn.cccn <- get.co.clustered.ptms(sub.cfn, ptm.cccn.edges, ptmtable)
return(sub.cfn.cccn)
}
@@ -717,7 +721,6 @@ ptms_to_cfn <- function(ptms, cfn = cfn.merged, pepsep = ";") {
#' @return Called for its side effects in Cytoscape.
#' @export
setNodeMapping <- function(cf=RCy3::getTableColumns('node')) {
- # require(RCy3)
RCy3::setBackgroundColorDefault("#949494") # grey 58
RCy3::setNodeShapeDefault("ELLIPSE")
RCy3::setNodeColorDefault("#F0FFFF") # azure1
@@ -748,7 +751,6 @@ setNodeMapping <- function(cf=RCy3::getTableColumns('node')) {
#' @return Called for its side effects in Cytoscape.
#' @export
setCorrEdgeAppearance <- function() {
- # require(RCy3)
RCy3::setEdgeLineWidthDefault(3)
RCy3::setEdgeColorDefault("#FFFFFF") # white
edgevalues <- RCy3::getTableColumns('edge',c('Weight'))
@@ -792,10 +794,9 @@ setCorrEdgeAppearance <- function() {
#' @return Called for its side effects in Cytoscape.
#' @export
setNodeColorToRatios <- function(plotcol){
- require(RCy3)
cf <- RCy3::getTableColumns('node')
- if(!(plotcol %in% getTableColumnNames('node'))){
- print (getTableColumnNames('node'))
+ if(!(plotcol %in% RCy3::getTableColumnNames('node'))){
+ print (RCy3::getTableColumnNames('node'))
cat("\n","\n","\t", "Which attribute will set node size and color?")
plotcol <- as.character(readLines(con = stdin(), n = 1))
}
@@ -833,9 +834,9 @@ setNodeColorToRatios <- function(plotcol){
#' @return Called for its side effects in Cytoscape.
#' @export
setNodeColorToRowz <- function(plotcol){
- cf <- getTableColumns('node')
- if(!(plotcol %in% getTableColumnNames('node'))){
- print (getTableColumnNames('node'))
+ cf <- RCy3::getTableColumns('node')
+ if(!(plotcol %in% RCy3::getTableColumnNames('node'))){
+ print (RCy3::getTableColumnNames('node'))
cat("\n","\n","\t", "Which attribute will set node size and color?")
plotcol <- as.character(readLines(con = stdin(), n = 1))
}
@@ -981,9 +982,6 @@ setNodeSizeColorIndependently <- function(sizeplotcol, colorplotcol, ratio=FALSE
#' @return Called for its side effects; creates a styled network in Cytoscape.
#' @export
GraphCfn <- function(cfn.edges, cfn.nodes, Network.title = "CFN", Network.collection = "PTMsToPathways", visual.style.name = "PTMsToPathways.style"){
- if(!requireNamespace("RCy3", quietly = TRUE)){
- stop("In order to use this function, please download RCy3 as described in the vignette, the readme, and the function documentation.")
- }
tryCatch({
RCy3::cytoscapePing()
}, error = function(e){
@@ -1136,6 +1134,4 @@ NodeEdgeKey <- function(visual.style.name = "PTMsToPathways.style") {
RCy3::copyVisualStyle("default", visual.style.name)
RCy3::setVisualStyle(visual.style.name)
message("Check the 'Node & Edge Key' network in Cytoscape: kinase sources PHOSPHORYLATION/pp, all edges labelled, all node-edge types illustrated.")
-}
-
-
+}
\ No newline at end of file
diff --git a/R/MakeCorrelationNetwork.R b/R/MakeCorrelationNetwork.R
index db3301c3..aade533e 100644
--- a/R/MakeCorrelationNetwork.R
+++ b/R/MakeCorrelationNetwork.R
@@ -87,7 +87,7 @@ MakeCorrelationNetwork <- function(adj.consensus.matrix, ptm.correlation.matrix)
# Sum correlations in one dimension, then the other dimension
gene.cccn2 <- dplyr::summarise(
- dplyr::group_by(gene.cccn, Gene.Name),
+ dplyr::group_by(gene.cccn, .data$Gene.Name),
dplyr::across(
tidyselect::where(is.numeric),
~ sum(.x, na.rm = TRUE)
diff --git a/R/imports.R b/R/imports.R
new file mode 100644
index 00000000..ad23b8cc
--- /dev/null
+++ b/R/imports.R
@@ -0,0 +1,2 @@
+#' @importFrom rlang .data
+NULL
\ No newline at end of file
diff --git a/R/sysdata.rda b/R/sysdata.rda
new file mode 100644
index 00000000..a3d0bd95
Binary files /dev/null and b/R/sysdata.rda differ
diff --git a/data-raw/function-key.R b/data-raw/function-key.R
index d3b9ed46..4eb1ff9f 100644
--- a/data-raw/function-key.R
+++ b/data-raw/function-key.R
@@ -9,4 +9,4 @@ function_key <- read.table(
fill = TRUE
)
-usethis::use_data(function_key, overwrite = TRUE)
\ No newline at end of file
+usethis::use_data(function_key, overwrite = TRUE, internal = TRUE)
\ No newline at end of file
diff --git a/man/BuildClusterFilteredNetwork.Rd b/man/BuildClusterFilteredNetwork.Rd
index 38e752e4..64a750a3 100644
--- a/man/BuildClusterFilteredNetwork.Rd
+++ b/man/BuildClusterFilteredNetwork.Rd
@@ -36,6 +36,7 @@ If either of these conditions are not met, then it will be removed from the list
This new, cluster filtered network is then assigned to the global namespace.
}
\examples{
-Example_Output <- BuildClusterFilteredNetwork(ex_gene_cccn_edges, ex_stringdb_edges, ex_genemania_edges)
+Example_Output <- BuildClusterFilteredNetwork(ex_gene_cccn_edges,
+ ex_stringdb_edges, ex_genemania_edges)
utils::head(Example_Output[[2]])
}
diff --git a/man/cytoscape.graph.PCN.pathways.Rd b/man/cytoscape.graph.PCN.pathways.Rd
index 57a1c87a..3c1a9999 100644
--- a/man/cytoscape.graph.PCN.pathways.Rd
+++ b/man/cytoscape.graph.PCN.pathways.Rd
@@ -4,11 +4,7 @@
\alias{cytoscape.graph.PCN.pathways}
\title{Graph a Pathway Crosstalk Network in Cytoscape}
\usage{
-cytoscape.graph.PCN.pathways(
- PCN = pathway.crosstalk.network,
- net.name,
- Jaccard.edges = TRUE
-)
+cytoscape.graph.PCN.pathways(PCN, net.name, Jaccard.edges = TRUE)
}
\arguments{
\item{PCN}{A data frame representing the pathway crosstalk network with columns
diff --git a/man/get.co.clustered.ptms.Rd b/man/get.co.clustered.ptms.Rd
index 62794ae6..5d27acfb 100644
--- a/man/get.co.clustered.ptms.Rd
+++ b/man/get.co.clustered.ptms.Rd
@@ -4,13 +4,15 @@
\alias{get.co.clustered.ptms}
\title{Retrieve co-clustered PTM CCCN edges for genes in an edge file}
\usage{
-get.co.clustered.ptms(edge.file, ptm.cccn.edges)
+get.co.clustered.ptms(edge.file, ptm.cccn.edges, ptmtable)
}
\arguments{
\item{edge.file}{A data frame edge list whose nodes are gene names.}
\item{ptm.cccn.edges}{A data frame of PTM co-expression correlation network
edges with PTM identifiers as node names.}
+
+\item{ptmtable}{A PTM data frame with PTM identifiers as row names and numeric condition columns.}
}
\value{
An edge data frame combining the original gene edges, co-clustered
diff --git a/man/make.cytoscape.node.file.Rd b/man/make.cytoscape.node.file.Rd
index ae498cb0..c884eb70 100644
--- a/man/make.cytoscape.node.file.Rd
+++ b/man/make.cytoscape.node.file.Rd
@@ -6,10 +6,11 @@
\usage{
make.cytoscape.node.file(
edge.file,
- funckey,
+ funckey = PTMsToPathways::function_key,
ptmtable,
include.gene.data = FALSE,
- include.coclustered.PTMs = FALSE
+ include.coclustered.PTMs = FALSE,
+ ptm.cccn.edges = NULL
)
}
\arguments{
@@ -27,6 +28,9 @@ summarised PTM values to the node table. Defaults to \code{FALSE}.}
\item{include.coclustered.PTMs}{Logical; if \code{TRUE}, add co-clustered
PTM nodes and their edges to the output. Defaults to \code{FALSE}.}
+
+\item{ptm.cccn.edges}{A data frame of PTM co-expression correlation network
+edges with PTM identifiers as node names, required if \code{include.coclustered.PTMs = TRUE}.}
}
\value{
A data frame of node attributes with an \code{id} column suitable
diff --git a/man/ptms_to_cfn.Rd b/man/ptms_to_cfn.Rd
index 10c0eda8..fd716d20 100644
--- a/man/ptms_to_cfn.Rd
+++ b/man/ptms_to_cfn.Rd
@@ -4,13 +4,18 @@
\alias{ptms_to_cfn}
\title{Extracts co-clustered PTM and gene network from a cluster filtered network object.}
\usage{
-ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";")
+ptms_to_cfn(ptms, cfn, ptm.cccn.edges, ptmtable, pepsep = ";")
}
\arguments{
\item{ptms}{Character vector of PTM site strings (e.g., \"TP53 p S15\")}
\item{cfn}{List or data frame representing the cluster filtered network (default: global cfn.merged)}
+\item{ptm.cccn.edges}{A data frame of PTM co-expression correlation network
+edges with PTM identifiers as node names}
+
+\item{ptmtable}{A data frame containing PTM identifiers as row names and numeric condition columns}
+
\item{pepsep}{Character used to split ambiguous PTM entries (default: \";\")}
}
\value{
@@ -31,7 +36,8 @@ cfn.merged <- data.frame(source = c("TP53", "BRCA1", "BRCA1", "MDM2"),
# Suppose filter.edges.0 and get.co.clustered.ptms are also defined and loaded
# The following returns the gene/PTM subnetwork
\dontrun{
-res <- ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";")
+res <- ptms_to_cfn(ptms, cfn = cfn.merged,
+ ptm.cccn.edges = ptm.cccn.edges, ptmtable = ptmtable, pepsep = ";")
print(res)
}
}
diff --git a/vignettes/BRCANetworks.Rmd b/vignettes/BRCANetworks.Rmd
index 9afb285e..edc18f27 100644
--- a/vignettes/BRCANetworks.Rmd
+++ b/vignettes/BRCANetworks.Rmd
@@ -18,7 +18,7 @@ output:
toc: true
toc_depth: '4'
vignette: >
- %\VignetteIndexEntry{PTMsToPathways}
+ %\VignetteIndexEntry{BRCANetworks}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
editor_options:
@@ -417,10 +417,11 @@ Cytoscape. This code graphs the CFN/CCCN from all these PTMs:
```{r eval = TRUE}
funckey <- function_key
-cfn.cccn <- ptms_to_cfn(mod63.clust.ptms, cfn = cfn.merged, pepsep = ";")
+cfn.cccn <- ptms_to_cfn(mod63.clust.ptms, cfn = cfn.merged, ptm.cccn.edges = ptm.cccn.edges, ptmtable = ptmtable, pepsep = ";")
cfn_cccn.nodes <- make.cytoscape.node.file(cfn.cccn, funckey, ptmtable,
include.gene.data = TRUE,
- include.coclustered.PTMs = TRUE)
+ include.coclustered.PTMs = TRUE,
+ ptm.cccn.edges = ptm.cccn.edges)
```
To graph in Cytoscape: