From 03bc88f00a4ef5c148d945efa52c9a4f567f5321 Mon Sep 17 00:00:00 2001 From: Sam El-Kamand Date: Wed, 7 Aug 2024 16:01:58 +1000 Subject: [PATCH 1/3] docs: added DOIs to CRAN packages --- paper/jats/paper.jats | 3 +++ paper/paper.bib | 7 +++++-- paper/paper.pdf | Bin 729603 -> 729639 bytes 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/paper/jats/paper.jats b/paper/jats/paper.jats index 2137c2f..30431c4 100644 --- a/paper/jats/paper.jats +++ b/paper/jats/paper.jats @@ -313,6 +313,7 @@ a Creative Commons Attribution 4.0 International License (CC BY Ggiraph: Make ’ggplot2’ graphics interactive 2024 https://davidgohel.github.io/ggiraph/ + 10.32614/CRAN.package.ggiraph @@ -323,6 +324,7 @@ a Creative Commons Attribution 4.0 International License (CC BY Patchwork: The composer of plots 2024 https://patchwork.data-imaginist.com + 10.32614/cran.package.patchwork @@ -335,6 +337,7 @@ a Creative Commons Attribution 4.0 International License (CC BY 2016 978-3-319-24277-4 https://ggplot2.tidyverse.org + 10.32614/CRAN.package.ggplot2 diff --git a/paper/paper.bib b/paper/paper.bib index 9219c99..77cdecf 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -45,7 +45,8 @@ @misc{gohel:2024 author = {David Gohel and Panagiotis Skintzos}, year = {2024}, note = {R package version 0.8.10}, - url = {https://davidgohel.github.io/ggiraph/} + url = {https://davidgohel.github.io/ggiraph/}, + doi = {10.32614/CRAN.package.ggiraph} } @misc{pedersen:2024, @@ -53,7 +54,8 @@ @misc{pedersen:2024 author = {Thomas Lin Pedersen}, year = {2024}, note = {R package version 1.2.0.9000}, - url = {https://patchwork.data-imaginist.com} + url = {https://patchwork.data-imaginist.com}, + doi = {10.32614/cran.package.patchwork} } @Book{wickham:2016, @@ -63,6 +65,7 @@ @Book{wickham:2016 year = {2016}, isbn = {978-3-319-24277-4}, url = {https://ggplot2.tidyverse.org}, + doi = {10.32614/CRAN.package.ggplot2} } diff --git a/paper/paper.pdf b/paper/paper.pdf index a919b2b2b8dc9104f6b19ea2966c12a1d54056a9..452ecaa6c6e3b8b1c7ea8323efd7d8019fef0504 100644 GIT binary patch delta 4087 zcma)9S5y;k*9fz(f$;x;Z1q6o|H3AddLS2- z=-s<0v=bbIlyO75xyT@(@-8wMI0ho)C%_*uf@JZ-0cm<&259 zd#z#0E+ByAZW%bBbYAqaw483sEv`qnqTu8Xfs)N)SXP@K6`SuBx3*RZhqj6hEmU7W5HFh%kZPrQ>spDyIJheGm zLD@Z=Kat}^g@i55&8IO)*GR8xVnrGl7;arLqMI;!GHy-k?)Yj9;#I!I{&{+tfzzfeM$8eXk8Pyl!<%);-BBm~FXy$xQZ;8YM$i{V3K3ng;zxG#J#qBX6P#4~ za|VOg&h|>8M`vWr^3ofzp`s3S$!aJb7bqHmajVQw6x6Q#aZP^R82ZWk`S0eE{>9Rg zp2aDZ>&7HDp_EqQezVmuJ_6v02uUfbdZ<~2p|qzB@MgZO8Qd7_0Tp~I7H5x0_pkl~V`66hOPu zy>=ljbRzv4JWL9oh1T3i5U=~niIujcCpz+VE?xzF#Y2NfrNyK0aTCT}-i@1Jdqx4P zlx@#qr_c9iR(D>g$7BlAz6CM$mw4KcD`;t42g+VM=M(w#DA+EEP8+w=j*r+QcxczoHSPBhb8^FiGh>2u*J&ZU}98o#cY7W>?lZ&=$e1Xobu ztV#`v=tsh{xD-3b604AOd|+1j-MAXyGzZzL`WO4BgGp)JS`3VUq!UajSg{ zTHlG38FKV$oB*{`OFFy=^*BGnI*C?JCYbN?L;#mb?V@C0Mg`_+c6&s@)-4I6|hM*w68EbXCAgLaFB6gKF&Mtvlf(&jMRXVpsKU(x{E((+%tLF`!k}GPjbF)uO zf`4}Negsjd`Pg?i(!5*IV3PEfNAu?DhmGW>%Hx~u?T(=?^ac+hQ>xn1N*Bxcq$_KWO13kF48AHlUEehOlbJgH zzG5ITBIWar=>bYH>?GMig5%G%+o|AeEorjXX=Tx^Z(Ln>C#MNZ~((k5@i?AAt#9#3lr4w0u!{{($#XPl| zyJtF-zk@zW-dW z`CRjh?&%_pIO*6to7_+VJ%P`2QXbO7DYgmI1sYMIK!0&1h4-_;^^q$~4)ey5*&eFH zCoP=jAqv(E1ikH~5wnP|dh>Jpjax@-awlS+o{sKFI>I|EleT5PzAOkki$I9t%Sk;y zdBd|9)l0$}oooF)rGmR!mZh{K!fDUks1w+FUtN>4-m8)iIph23(&wM&s#1KpF*-+Wi}To4DYr5qR^sW*y4~Rz;5F#RVU6z;Y-pt zjtw7uXSI|NurKgO6DG!7EvB<8w;?`u3&W!phGSHI%I8+xGjo|Vj z2br-mY}b$@qrd5GQq#rS5N;irhltk0d#waXq)4h@-D4^3+-%2<(BFOh>yNkhXw@Fh zB`Tox;be-1Sg^reAKO7ec~5=5rQ_GlYCjdu3-oyq-mMcl$dl8Ks-eZ2RX>i*ncuN* z7uuFti+$U>%gam76*~-v@k-(=OS{4j;T5)W@$orQ(%keG59-4ia;}8A(4XzeLw8Ed z3mn+RS@kL1g}_FYKy4S_meI#-rDA%Xc=Vr>;T_Wpa~It@cSxLbl{nR-*`CZL@8g)58s*q)i8ye2%BPHW|rRcl;12%+n`mqwxm83_bzRb z<^`z{lHHE0&9j`DXjb$^GCzKYzUMtzjk$EVIK#tVq4>PfewRgIl{4JBs8L-&ki+hI z7#-i1p<#}`;&FVQ51!e@z)^8T%c@pvM#SS)xT(FEN=sav`C5}!dP`7e!PnWp_ zFP%AVn6g~Umc6;OL-|&Vz>6QzbH=7jx3eV6YeAmbd6p)N;n~?U!rV&r$v^V+djRLQ z_Chq(h{v3($3o$6a|AXJ&v8^X{Yjhf6~%M+Xa;=Bh`+9Hyh*!AdKXKK-_Q`3W|_ZH&r!~^>=dic5-)> zb$9m+aPs#cR1iRAe@pTpg6wHga9Mc-iZDb3ss3FKEWmAd^AX02G37^#7yV6@aX+L1hsLwBSFt zl!aoT{}hDCBA{@>Xg)~&|I}*YD+F;+5$@%H=s6Jxd0Ch|R1hwYkww8Uf(R5u76wQC z&yfFqKz|>n$U`%9+v!$S?d?_a~_k+Va3fn_-Q=XBDLx~Y3{q!vUE)Zinqh$=zQAUUAdskRG2o;s$$fiS` zpS1t|S|nUza?o_Hm%?i=%jQdUQ#aQv*{8!5)_BcFbkT+B?6lpwO<{Ums;x4brlLgs*0T!X#j8TjCeOm%LZ$N#ZdW|JK2bWI zvG%keQdBbMMkKTD&p}qqi5*8e_?6XDaFylzIFgpAjIh2Dhr<9&WUXXiy0Qc>@;hvu}T!{xJIN%OwdwuglrI zOs0TnkCLG&kc;0rLvIk`ESmk)i6`6KC|)VmIL%6#%?#iDOxbOpmbmY-^JdKXP7Zk! zmvF$rFyzSn8E&}enBkd1yF{G#G)Q2=eW{o_SZ2l%@+XIS9Tm4=lOMYmp1b4;z+@~8 z=BdliM9uKD+HIK+ZHE_n+KiKP3#`l0`I{%vL8OO=k2ZhN;gp96AJfjc)-0$}$0FRW zT<|FLw<)%~$31uKuyya?fI6?|E=v!|+k1Qkz;pXQG&z?neI~WB`Wsw8Qz3nyhG}r_ hfR_fh>DlhzIis_ARa{7z6JihqqA?&aSkqVw^bdc>YTy6> delta 4085 zcmaitbyyP&+r?#sZj>S*IYJO51}oSI32BCel#~LaV@N5;7$6`>=Z185Neqyb5=@xvS>-)azd*8pF_d5TabD!UJ?&2P?mpx)Zp%kHjP|8rMQ0h>c(5s=>>Vdc# zTBM<*lnfj$14WtwxSO0&qKP z6bfsL7Ppa-wiZX&*~9+V{eAztf!RReXe2qd9{7m@APFa1HUc*$l6YxZ32o*Bu>#HX zZ8Ii4j0I+#4Oe0So=7=z;}0oP68$+WCK$iFZJs9_nHv#pA>yK^felyY7koWvJ2~L|LO4IMv$I~0 zt8BP1Wq)dklC_H&gJV5OPCGHgB!1-Bt*8Eot6Ejoi?h}v_HswX%^u)S!gNgfL^I=97liig(>M+i6$9aoJCPo}@Hst2%b z+K29XnsGx-b{|&>BSvP=N`g|~->*1u-H@G`PB%%NF+WnCO7UR%s$8`^2K_NvYs$-{ zEkF4Uzg{u)P?xiS3F^1mu`BBq;NJLZuS)oONF2$_R8u5<* zdO2^JOf+CD`klNHA67dUpT_9!W(1x;vA7v9?vfh0AvBLZO?HS%T;J7P+^>)g2o5^M$|kF z=0%cxZWF&W8W~o?T#Y~ExtDli^aUR&9_h`B)Qn{3y`53nZOU0MS66!Vu2f+|H{&K> zLknrS$>dW2fS`%+jm#e+*;wY`#4w*P}OGIE`; z3<4PJ&AWGQU`3>=Dk<@QWg$YAO|5RVAl5yr;k}u*k$h~&d(jKuRQ|djN72O8$zF8a zT+GKP=P3*(Er@8n(x&FF+Jx5kax5(mO%Df)n87NV2yc#yC_G^@pdH$-%JhY#EZdwI z5cf7|ttea4+4EjRiADb40)_iap@?Bu9%h^Z#ZgF*kY{qR7xIAPq!Z0kDU9>vBq;J*;GC8V+1Rd z^iF1kG%^9XP8DbFOwm}fRxmEUX5a1pEb&T|kY{=rJ5GTCKEN;kRlperH7sQ<^PR?i z3~yyL@DZz>B?f)C8K+!V3Y05n+80+z8O_#!W$Y^ZPuRTI+F1tX`V9I0_^7zo6B}HS zQNpg5KA;WERC!q(+tMh-Q!U!yoQ#fmnEhdV?u+iBD|`R*ES1zp3rU0xUfw2sSq*AYhKxr7xI$$sqm<)+Izz2J*Qt zFEBYzu5`FN`ZvwT_A~<&y>e-@8&!0Tpn2KIuGKZw10O&Z`#jx2hk#ve^4N{!;T^Um zwDZX9;wk>sR9u?v$Cz9x8IH}?c9MkGEF6o+9`dj-mn=|{a4j4ZtYI}eaTBbW{83k~{gnr2$J@J`K5qE( zK*a1uJ&&f_^B5_FxRy#CDXisXc?z$M#nznZ3@_RQ-*7A>otdO_MiF(0kMuDnSSF6N zyi}-Hsf9Z28 zH2sb9t%#ffcbi{>31SJ6QxjdLgz&D^v}YA|5__@jV%u^fTWd8J2Lqm6HN+By%P&pY z83uIu6sYTcM@fYOY5R75D-`hov148WS!Q&6pTUf4q#0Piqd4Z02>5vZH9eP6L77Rb zLyvq9s=fqu(ERy%-U@x~FIk}lmaS3_&vlnadAmPqUqvBGxozI+7r0z+Cx~|lexKq% z++b_jz6;HZ# zJa(w`V%S)pjH+E@axMBzosquSfqGjP4(|Yr4Sp14C1aSg4}>iUU;)kd~L0%4kME!{kJl1C|9k}Wt!4TV%NYimJ#brAjGxKL*nc1U@$Y_#6m zJ$u146(h=D*bhGhIp)jug>I8~vD%}^2$IE!uz)eITh%b5eZ!T$^x&L2y1TMEoN_e_ z%871{7`;)5ebh$J!Wx|ckUlUBu1OD^!b?#tJ)d`I{f#1Q*7!Jm^9o!l!d?BPJt+Qy zDW+i1y?pL%;a$Agu;?T{pv3Iy!woOZoY9|AV=I6MMTo~IRzc8Q3C>L1R$%)ExEhpP zOkeHA18I5_vl(Cn1GMmT7S34P ze7H0D=%~)()rPW`kz#F`35Cb{s%p6LkN2Eet5Rtz&HaD=kOsPvQ45=JAa{tmZ+Txmb;QzpO#VOtx1ItzU}a}X=t{StB+v2yFi_` z5AX%s4~}x8f~XCYI815Bm1s<_!jxD|8Q&@~e4yrx_{hN$2xnVMsBB5^Kvx)p+^DDv zhU)o?3E@MlFLki(aXWyeR&2NsNodv6hc@jhKEO+{n2uh*r(Qs4hoZfcafo_9Na5O* z;7;nbq;`bh2u(tJfSQ5iCZW$zlU768GMQPq#ZO~gd0gBtQCX9m6<>cXG{Jp8AvfLo zd`sqim(4i$67%K*@{nr$uk6K2!Giu40oBAT6vXN7royp+YJxbgo&jR^y^BC^yttEM zg7|4Y9r5X##nDx)C}f#dunQJV{gf9h5XACCP=iX7m%Rc|-o+6QAZT?-)o?QhbLX&a zQH5DlDwU-KRj#n1dtXd)Q!<3ac{VV(6@7q0+}4z2{YPWLh+OqIqfwZLc@_^4XC1&->uK|BAwuxTU(SVD0dqv{L!`*_PR$^Ez^VW;`3S+nDEbT_K$Yz==SF7`XrB9rpHKZS2qW@;D0L> zb%d}-*wOIZW`V`cd1y4v3|-G=+^?tFMDB|v_yxwYcj0YQ?hQqC50zuq#6fM^)_43? z*YNWD$f&e3+rXXI8STOc`*0xz+J0~5{y39g-kEkG;1EX4jznK({w3wGbDj?Il8=@b Oh=76w1yyy`K>q^i36OaJ From c392b3160d38a820404f5d9ef5ed86df1c15689b Mon Sep 17 00:00:00 2001 From: Sam El-Kamand Date: Wed, 7 Aug 2024 16:12:32 +1000 Subject: [PATCH 2/3] docs: moved community contribution guidelines to CONTRIBUTING.md --- CONTRIBUTING.md | 74 ++++++++++++++++++++++++++++++++++++++++++++++ README.Rmd | 74 +--------------------------------------------- README.md | 78 ++----------------------------------------------- 3 files changed, 77 insertions(+), 149 deletions(-) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..46b8003 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,74 @@ +### Contribute to the Software + +There are many ways to contribute to ggoncoplot. + +1. Request features you would like to by [creating new issues on + github](https://github.com/selkamand/ggoncoplot/issues) +2. [Make your visualisation packages ggoncoplot-compatible] +3. [Directly contribute to the ggoncoplot codebase] + +#### Make your visualisation packages ggoncoplot-compatible + +If your package produces ggplots that you would like to interactively +link with ggoncoplot, consider converting your geoms to their ggiraph +interactive equivalents and adding a data_id based on a sample +identifier column in the dataset. That way end-users can create a +data-linked oncoplot composed with your packages plots using patchwork +([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages)) + +#### Directly contribute to the ggoncoplot codebase + +We welcome contributions from the community to enhance and expand the +functionality of `ggoncoplot`. Whether you want to fix a bug, add new +features, improve documentation, or optimize performance, your efforts +are highly valued. To get started: + +1. **Fork the Repository**: Click on the 'Fork' button at the top right + of this page to create a copy of the repository in your GitHub + account. + +2. **Clone the Repository**: Use `git clone` to clone your forked + repository to your local machine. + + ``` bash + git clone https://github.com/selkamand/ggoncoplot.git + ``` + +3. **Create a Branch** + + ``` bash + git checkout -b feature-name + ``` + +4. **Make Changes**: Implement your changes in the new branch + +5. **Commit and Push**: Commit your changes and push the branch to your + forked repository. + +6. **Create a Pull Request**: Go to the original repository and open a + pull request from your branch. Please provide a clear description of + your changes and any relevant issues or discussions. + +### Report Issues or Problems with the Software + +If you encounter any issues, bugs, or have suggestions for improvements, +please report them using the [GitHub Issues Tab](https://github.com/selkamand/ggoncoplot/issues/). + +### Seek Support + +For any questions or support regarding the use of ggoncoplot you can: + +- **Check the Documentation**: Comprehensive documentation is + available [here](https://selkamand.github.io/ggoncoplot/index.html). + +- **Create a** [new + issue](https://github.com/selkamand/ggoncoplot/issues/new) with your + query. + +- **Browse Existing Issues**: Check the + [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see + if your query has been addressed. + +- **Contact Us**: If you need direct assistance, please [contact the + maintainers + directly](mailto:selkamand@ccia.org.au?subject=ggoncoplot) diff --git a/README.Rmd b/README.Rmd index 3c339c7..355eaf0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -140,77 +140,5 @@ during the early stages of ggoncoplot development. ## Community Contributions -### Contribute to the Software +All types of contributions are encouraged and valued. See our [guide to community contributions](CONTRIBUTING.md) for different ways to help. -There are many ways to contribute to ggoncoplot. - -1. Request features you would like to by [creating new issues on - github](https://github.com/selkamand/ggoncoplot/issues) -2. [Make your visualisation packages ggoncoplot-compatible] -3. [Directly contribute to the ggoncoplot codebase] - -#### Make your visualisation packages ggoncoplot-compatible - -If your package produces ggplots that you would like to interactively -link with ggoncoplot, consider converting your geoms to their ggiraph -interactive equivalents and adding a data_id based on a sample -identifier column in the dataset. That way end-users can create a -data-linked oncoplot composed with your packages plots using patchwork -([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages)) - -#### Directly contribute to the ggoncoplot codebase - -We welcome contributions from the community to enhance and expand the -functionality of `ggoncoplot`. Whether you want to fix a bug, add new -features, improve documentation, or optimize performance, your efforts -are highly valued. To get started: - -1. **Fork the Repository**: Click on the 'Fork' button at the top right - of this page to create a copy of the repository in your GitHub - account. - -2. **Clone the Repository**: Use `git clone` to clone your forked - repository to your local machine. - - ``` bash - git clone https://github.com/selkamand/ggoncoplot.git - ``` - -3. **Create a Branch** - - ``` bash - git checkout -b feature-name - ``` - -4. **Make Changes**: Implement your changes in the new branch - -5. **Commit and Push**: Commit your changes and push the branch to your - forked repository. - -6. **Create a Pull Request**: Go to the original repository and open a - pull request from your branch. Please provide a clear description of - your changes and any relevant issues or discussions. - -### Report Issues or Problems with the Software - -If you encounter any issues, bugs, or have suggestions for improvements, -please report them using the [GitHub Issues Tab](https://github.com/selkamand/ggoncoplot/issues/). - -### Seek Support - -For any questions or support regarding the use of ggoncoplot you can: - -- **Check the Documentation**: Comprehensive documentation is - available [here](https://selkamand.github.io/ggoncoplot/index.html). - -- **Create a** [new - issue](https://github.com/selkamand/ggoncoplot/issues/new) with your - query. - -- **Browse Existing Issues**: Check the - [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see - if your query has been addressed. - -- **Contact Us**: If you need direct assistance, please [contact the - maintainers - directly](mailto:selkamand@ccia.org.au?subject=ggoncoplot) diff --git a/README.md b/README.md index 76f661f..7c5665d 100644 --- a/README.md +++ b/README.md @@ -172,79 +172,5 @@ during the early stages of ggoncoplot development. ## Community Contributions -### Contribute to the Software - -There are many ways to contribute to ggoncoplot. - -1. Request features you would like to by [creating new issues on - github](https://github.com/selkamand/ggoncoplot/issues) -2. [Make your visualisation packages - ggoncoplot-compatible](#make-your-visualisation-packages-ggoncoplot-compatible) -3. [Directly contribute to the ggoncoplot - codebase](#directly-contribute-to-the-ggoncoplot-codebase) - -#### Make your visualisation packages ggoncoplot-compatible - -If your package produces ggplots that you would like to interactively -link with ggoncoplot, consider converting your geoms to their ggiraph -interactive equivalents and adding a data_id based on a sample -identifier column in the dataset. That way end-users can create a -data-linked oncoplot composed with your packages plots using patchwork -([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages)) - -#### Directly contribute to the ggoncoplot codebase - -We welcome contributions from the community to enhance and expand the -functionality of `ggoncoplot`. Whether you want to fix a bug, add new -features, improve documentation, or optimize performance, your efforts -are highly valued. To get started: - -1. **Fork the Repository**: Click on the ‘Fork’ button at the top right - of this page to create a copy of the repository in your GitHub - account. - -2. **Clone the Repository**: Use `git clone` to clone your forked - repository to your local machine. - - ``` bash - git clone https://github.com/selkamand/ggoncoplot.git - ``` - -3. **Create a Branch** - - ``` bash - git checkout -b feature-name - ``` - -4. **Make Changes**: Implement your changes in the new branch - -5. **Commit and Push**: Commit your changes and push the branch to your - forked repository. - -6. **Create a Pull Request**: Go to the original repository and open a - pull request from your branch. Please provide a clear description of - your changes and any relevant issues or discussions. - -### Report Issues or Problems with the Software - -If you encounter any issues, bugs, or have suggestions for improvements, -please report them using the [GitHub Issues -Tab](https://github.com/selkamand/ggoncoplot/issues/). - -### Seek Support - -For any questions or support regarding the use of ggoncoplot you can: - -- **Check the Documentation**: Comprehensive documentation is available - [here](https://selkamand.github.io/ggoncoplot/index.html). - -- **Create a** [new - issue](https://github.com/selkamand/ggoncoplot/issues/new) with your - query. - -- **Browse Existing Issues**: Check the - [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see - if your query has been addressed. - -- **Contact Us**: If you need direct assistance, please [contact the - maintainers directly](mailto:selkamand@ccia.org.au?subject=ggoncoplot) +All types of contributions are encouraged and valued. See our [guide to +community contributions](CONTRIBUTING.md) for different ways to help. From 1894e20db85576e6923b2839e9243092f92d3436 Mon Sep 17 00:00:00 2001 From: Sam El-Kamand Date: Wed, 7 Aug 2024 16:13:14 +1000 Subject: [PATCH 3/3] fix: added CONTRIBUTING.md to Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 8957f27..17ca0ba 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,3 +10,4 @@ ^Meta$ ^codecov\.yml$ ^paper +CONTRIBUTING.md