class: center, middle, inverse, title-slide # Publication/Presentation-ready Tables ### Janani Ravi ### Michigan State University + R-Ladies East Lansing ### 2021-05-09 --- class: center, bottom background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg) Slides made with [`xaringan`](https://github.com/yihui/xaringan) (Yihui Xie) and [R-Ladies theme](https://alison.rbind.io/project/rladies-xaringan/) (Allison Hill). --- class: inverse, center, middle # Overview --- class: center, top # GT <img src="https://gt.rstudio.com/reference/figures/gt_parts_of_a_table.svg" width="70%" /> --- class: center, top # knitr <img src="https://db.yihui.org/imgur/yYw46aF.jpg" height="70%" /> --- class: center, top # rmarkdown <img src="https://i2.wp.com/jessecambon.github.io/images/hex-rmarkdown.png?w=200&ssl=1" height="70%" /> --- class: center, top # DT & datatables <img src="https://shiny.rstudio.com/images/datatable.png" width="50%" /> --- class: center, top # Explore later: flextable <img src="https://ardata-fr.github.io/flextable-book/assets/img/flextable_functions.svg" width="70%" /> --- class: inverse, middle, center # Let's create a few cool tables! --- # Tables w/ `knitr` If you want to generate a table, make sure it is in the HTML format (instead of Markdown or other formats), e.g., ```r knitr::kable(head(iris), format = 'html') ``` <table> <thead> <tr> <th style="text-align:right;"> Sepal.Length </th> <th style="text-align:right;"> Sepal.Width </th> <th style="text-align:right;"> Petal.Length </th> <th style="text-align:right;"> Petal.Width </th> <th style="text-align:left;"> Species </th> </tr> </thead> <tbody> <tr> <td style="text-align:right;"> 5.1 </td> <td style="text-align:right;"> 3.5 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;"> 4.9 </td> <td style="text-align:right;"> 3.0 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;"> 4.7 </td> <td style="text-align:right;"> 3.2 </td> <td style="text-align:right;"> 1.3 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;"> 4.6 </td> <td style="text-align:right;"> 3.1 </td> <td style="text-align:right;"> 1.5 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;"> 5.0 </td> <td style="text-align:right;"> 3.6 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;"> 5.4 </td> <td style="text-align:right;"> 3.9 </td> <td style="text-align:right;"> 1.7 </td> <td style="text-align:right;"> 0.4 </td> <td style="text-align:left;"> setosa </td> </tr> </tbody> </table> --- # Tables w/ `rmarkdown` ```r paged_table(iris) ``` <div data-pagedtable="false"> <script data-pagedtable-source type="application/json"> {"columns":[{"label":["Sepal.Length"],"name":[1],"type":["dbl"],"align":["right"]},{"label":["Sepal.Width"],"name":[2],"type":["dbl"],"align":["right"]},{"label":["Petal.Length"],"name":[3],"type":["dbl"],"align":["right"]},{"label":["Petal.Width"],"name":[4],"type":["dbl"],"align":["right"]},{"label":["Species"],"name":[5],"type":["fct"],"align":["left"]}],"data":[{"1":"5.1","2":"3.5","3":"1.4","4":"0.2","5":"setosa"},{"1":"4.9","2":"3.0","3":"1.4","4":"0.2","5":"setosa"},{"1":"4.7","2":"3.2","3":"1.3","4":"0.2","5":"setosa"},{"1":"4.6","2":"3.1","3":"1.5","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.6","3":"1.4","4":"0.2","5":"setosa"},{"1":"5.4","2":"3.9","3":"1.7","4":"0.4","5":"setosa"},{"1":"4.6","2":"3.4","3":"1.4","4":"0.3","5":"setosa"},{"1":"5.0","2":"3.4","3":"1.5","4":"0.2","5":"setosa"},{"1":"4.4","2":"2.9","3":"1.4","4":"0.2","5":"setosa"},{"1":"4.9","2":"3.1","3":"1.5","4":"0.1","5":"setosa"},{"1":"5.4","2":"3.7","3":"1.5","4":"0.2","5":"setosa"},{"1":"4.8","2":"3.4","3":"1.6","4":"0.2","5":"setosa"},{"1":"4.8","2":"3.0","3":"1.4","4":"0.1","5":"setosa"},{"1":"4.3","2":"3.0","3":"1.1","4":"0.1","5":"setosa"},{"1":"5.8","2":"4.0","3":"1.2","4":"0.2","5":"setosa"},{"1":"5.7","2":"4.4","3":"1.5","4":"0.4","5":"setosa"},{"1":"5.4","2":"3.9","3":"1.3","4":"0.4","5":"setosa"},{"1":"5.1","2":"3.5","3":"1.4","4":"0.3","5":"setosa"},{"1":"5.7","2":"3.8","3":"1.7","4":"0.3","5":"setosa"},{"1":"5.1","2":"3.8","3":"1.5","4":"0.3","5":"setosa"},{"1":"5.4","2":"3.4","3":"1.7","4":"0.2","5":"setosa"},{"1":"5.1","2":"3.7","3":"1.5","4":"0.4","5":"setosa"},{"1":"4.6","2":"3.6","3":"1.0","4":"0.2","5":"setosa"},{"1":"5.1","2":"3.3","3":"1.7","4":"0.5","5":"setosa"},{"1":"4.8","2":"3.4","3":"1.9","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.0","3":"1.6","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.4","3":"1.6","4":"0.4","5":"setosa"},{"1":"5.2","2":"3.5","3":"1.5","4":"0.2","5":"setosa"},{"1":"5.2","2":"3.4","3":"1.4","4":"0.2","5":"setosa"},{"1":"4.7","2":"3.2","3":"1.6","4":"0.2","5":"setosa"},{"1":"4.8","2":"3.1","3":"1.6","4":"0.2","5":"setosa"},{"1":"5.4","2":"3.4","3":"1.5","4":"0.4","5":"setosa"},{"1":"5.2","2":"4.1","3":"1.5","4":"0.1","5":"setosa"},{"1":"5.5","2":"4.2","3":"1.4","4":"0.2","5":"setosa"},{"1":"4.9","2":"3.1","3":"1.5","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.2","3":"1.2","4":"0.2","5":"setosa"},{"1":"5.5","2":"3.5","3":"1.3","4":"0.2","5":"setosa"},{"1":"4.9","2":"3.6","3":"1.4","4":"0.1","5":"setosa"},{"1":"4.4","2":"3.0","3":"1.3","4":"0.2","5":"setosa"},{"1":"5.1","2":"3.4","3":"1.5","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.5","3":"1.3","4":"0.3","5":"setosa"},{"1":"4.5","2":"2.3","3":"1.3","4":"0.3","5":"setosa"},{"1":"4.4","2":"3.2","3":"1.3","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.5","3":"1.6","4":"0.6","5":"setosa"},{"1":"5.1","2":"3.8","3":"1.9","4":"0.4","5":"setosa"},{"1":"4.8","2":"3.0","3":"1.4","4":"0.3","5":"setosa"},{"1":"5.1","2":"3.8","3":"1.6","4":"0.2","5":"setosa"},{"1":"4.6","2":"3.2","3":"1.4","4":"0.2","5":"setosa"},{"1":"5.3","2":"3.7","3":"1.5","4":"0.2","5":"setosa"},{"1":"5.0","2":"3.3","3":"1.4","4":"0.2","5":"setosa"},{"1":"7.0","2":"3.2","3":"4.7","4":"1.4","5":"versicolor"},{"1":"6.4","2":"3.2","3":"4.5","4":"1.5","5":"versicolor"},{"1":"6.9","2":"3.1","3":"4.9","4":"1.5","5":"versicolor"},{"1":"5.5","2":"2.3","3":"4.0","4":"1.3","5":"versicolor"},{"1":"6.5","2":"2.8","3":"4.6","4":"1.5","5":"versicolor"},{"1":"5.7","2":"2.8","3":"4.5","4":"1.3","5":"versicolor"},{"1":"6.3","2":"3.3","3":"4.7","4":"1.6","5":"versicolor"},{"1":"4.9","2":"2.4","3":"3.3","4":"1.0","5":"versicolor"},{"1":"6.6","2":"2.9","3":"4.6","4":"1.3","5":"versicolor"},{"1":"5.2","2":"2.7","3":"3.9","4":"1.4","5":"versicolor"},{"1":"5.0","2":"2.0","3":"3.5","4":"1.0","5":"versicolor"},{"1":"5.9","2":"3.0","3":"4.2","4":"1.5","5":"versicolor"},{"1":"6.0","2":"2.2","3":"4.0","4":"1.0","5":"versicolor"},{"1":"6.1","2":"2.9","3":"4.7","4":"1.4","5":"versicolor"},{"1":"5.6","2":"2.9","3":"3.6","4":"1.3","5":"versicolor"},{"1":"6.7","2":"3.1","3":"4.4","4":"1.4","5":"versicolor"},{"1":"5.6","2":"3.0","3":"4.5","4":"1.5","5":"versicolor"},{"1":"5.8","2":"2.7","3":"4.1","4":"1.0","5":"versicolor"},{"1":"6.2","2":"2.2","3":"4.5","4":"1.5","5":"versicolor"},{"1":"5.6","2":"2.5","3":"3.9","4":"1.1","5":"versicolor"},{"1":"5.9","2":"3.2","3":"4.8","4":"1.8","5":"versicolor"},{"1":"6.1","2":"2.8","3":"4.0","4":"1.3","5":"versicolor"},{"1":"6.3","2":"2.5","3":"4.9","4":"1.5","5":"versicolor"},{"1":"6.1","2":"2.8","3":"4.7","4":"1.2","5":"versicolor"},{"1":"6.4","2":"2.9","3":"4.3","4":"1.3","5":"versicolor"},{"1":"6.6","2":"3.0","3":"4.4","4":"1.4","5":"versicolor"},{"1":"6.8","2":"2.8","3":"4.8","4":"1.4","5":"versicolor"},{"1":"6.7","2":"3.0","3":"5.0","4":"1.7","5":"versicolor"},{"1":"6.0","2":"2.9","3":"4.5","4":"1.5","5":"versicolor"},{"1":"5.7","2":"2.6","3":"3.5","4":"1.0","5":"versicolor"},{"1":"5.5","2":"2.4","3":"3.8","4":"1.1","5":"versicolor"},{"1":"5.5","2":"2.4","3":"3.7","4":"1.0","5":"versicolor"},{"1":"5.8","2":"2.7","3":"3.9","4":"1.2","5":"versicolor"},{"1":"6.0","2":"2.7","3":"5.1","4":"1.6","5":"versicolor"},{"1":"5.4","2":"3.0","3":"4.5","4":"1.5","5":"versicolor"},{"1":"6.0","2":"3.4","3":"4.5","4":"1.6","5":"versicolor"},{"1":"6.7","2":"3.1","3":"4.7","4":"1.5","5":"versicolor"},{"1":"6.3","2":"2.3","3":"4.4","4":"1.3","5":"versicolor"},{"1":"5.6","2":"3.0","3":"4.1","4":"1.3","5":"versicolor"},{"1":"5.5","2":"2.5","3":"4.0","4":"1.3","5":"versicolor"},{"1":"5.5","2":"2.6","3":"4.4","4":"1.2","5":"versicolor"},{"1":"6.1","2":"3.0","3":"4.6","4":"1.4","5":"versicolor"},{"1":"5.8","2":"2.6","3":"4.0","4":"1.2","5":"versicolor"},{"1":"5.0","2":"2.3","3":"3.3","4":"1.0","5":"versicolor"},{"1":"5.6","2":"2.7","3":"4.2","4":"1.3","5":"versicolor"},{"1":"5.7","2":"3.0","3":"4.2","4":"1.2","5":"versicolor"},{"1":"5.7","2":"2.9","3":"4.2","4":"1.3","5":"versicolor"},{"1":"6.2","2":"2.9","3":"4.3","4":"1.3","5":"versicolor"},{"1":"5.1","2":"2.5","3":"3.0","4":"1.1","5":"versicolor"},{"1":"5.7","2":"2.8","3":"4.1","4":"1.3","5":"versicolor"},{"1":"6.3","2":"3.3","3":"6.0","4":"2.5","5":"virginica"},{"1":"5.8","2":"2.7","3":"5.1","4":"1.9","5":"virginica"},{"1":"7.1","2":"3.0","3":"5.9","4":"2.1","5":"virginica"},{"1":"6.3","2":"2.9","3":"5.6","4":"1.8","5":"virginica"},{"1":"6.5","2":"3.0","3":"5.8","4":"2.2","5":"virginica"},{"1":"7.6","2":"3.0","3":"6.6","4":"2.1","5":"virginica"},{"1":"4.9","2":"2.5","3":"4.5","4":"1.7","5":"virginica"},{"1":"7.3","2":"2.9","3":"6.3","4":"1.8","5":"virginica"},{"1":"6.7","2":"2.5","3":"5.8","4":"1.8","5":"virginica"},{"1":"7.2","2":"3.6","3":"6.1","4":"2.5","5":"virginica"},{"1":"6.5","2":"3.2","3":"5.1","4":"2.0","5":"virginica"},{"1":"6.4","2":"2.7","3":"5.3","4":"1.9","5":"virginica"},{"1":"6.8","2":"3.0","3":"5.5","4":"2.1","5":"virginica"},{"1":"5.7","2":"2.5","3":"5.0","4":"2.0","5":"virginica"},{"1":"5.8","2":"2.8","3":"5.1","4":"2.4","5":"virginica"},{"1":"6.4","2":"3.2","3":"5.3","4":"2.3","5":"virginica"},{"1":"6.5","2":"3.0","3":"5.5","4":"1.8","5":"virginica"},{"1":"7.7","2":"3.8","3":"6.7","4":"2.2","5":"virginica"},{"1":"7.7","2":"2.6","3":"6.9","4":"2.3","5":"virginica"},{"1":"6.0","2":"2.2","3":"5.0","4":"1.5","5":"virginica"},{"1":"6.9","2":"3.2","3":"5.7","4":"2.3","5":"virginica"},{"1":"5.6","2":"2.8","3":"4.9","4":"2.0","5":"virginica"},{"1":"7.7","2":"2.8","3":"6.7","4":"2.0","5":"virginica"},{"1":"6.3","2":"2.7","3":"4.9","4":"1.8","5":"virginica"},{"1":"6.7","2":"3.3","3":"5.7","4":"2.1","5":"virginica"},{"1":"7.2","2":"3.2","3":"6.0","4":"1.8","5":"virginica"},{"1":"6.2","2":"2.8","3":"4.8","4":"1.8","5":"virginica"},{"1":"6.1","2":"3.0","3":"4.9","4":"1.8","5":"virginica"},{"1":"6.4","2":"2.8","3":"5.6","4":"2.1","5":"virginica"},{"1":"7.2","2":"3.0","3":"5.8","4":"1.6","5":"virginica"},{"1":"7.4","2":"2.8","3":"6.1","4":"1.9","5":"virginica"},{"1":"7.9","2":"3.8","3":"6.4","4":"2.0","5":"virginica"},{"1":"6.4","2":"2.8","3":"5.6","4":"2.2","5":"virginica"},{"1":"6.3","2":"2.8","3":"5.1","4":"1.5","5":"virginica"},{"1":"6.1","2":"2.6","3":"5.6","4":"1.4","5":"virginica"},{"1":"7.7","2":"3.0","3":"6.1","4":"2.3","5":"virginica"},{"1":"6.3","2":"3.4","3":"5.6","4":"2.4","5":"virginica"},{"1":"6.4","2":"3.1","3":"5.5","4":"1.8","5":"virginica"},{"1":"6.0","2":"3.0","3":"4.8","4":"1.8","5":"virginica"},{"1":"6.9","2":"3.1","3":"5.4","4":"2.1","5":"virginica"},{"1":"6.7","2":"3.1","3":"5.6","4":"2.4","5":"virginica"},{"1":"6.9","2":"3.1","3":"5.1","4":"2.3","5":"virginica"},{"1":"5.8","2":"2.7","3":"5.1","4":"1.9","5":"virginica"},{"1":"6.8","2":"3.2","3":"5.9","4":"2.3","5":"virginica"},{"1":"6.7","2":"3.3","3":"5.7","4":"2.5","5":"virginica"},{"1":"6.7","2":"3.0","3":"5.2","4":"2.3","5":"virginica"},{"1":"6.3","2":"2.5","3":"5.0","4":"1.9","5":"virginica"},{"1":"6.5","2":"3.0","3":"5.2","4":"2.0","5":"virginica"},{"1":"6.2","2":"3.4","3":"5.4","4":"2.3","5":"virginica"},{"1":"5.9","2":"3.0","3":"5.1","4":"1.8","5":"virginica"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}} </script> </div> --- # Tables w/ `kableExtra` ```r iris %>% head %>% kable(caption = "Table 1. Annotate with kableExtra") %>% kable_styling(c("striped", "hover", "condensed"), full_width = F, position = "left") %>% add_header_above(c("categorical"=1, "numerical" = 4)) %>% column_spec(1, bold = T) %>% row_spec(0, italic = T) ``` <table class="table table-striped table-hover table-condensed" style="width: auto !important; "> <caption>Table 1. Annotate with kableExtra</caption> <thead> <tr> <th style="border-bottom:hidden;padding-bottom:0; padding-left:3px;padding-right:3px;text-align: center; " colspan="1"><div style="border-bottom: 1px solid #ddd; padding-bottom: 5px; ">categorical</div></th> <th style="border-bottom:hidden;padding-bottom:0; padding-left:3px;padding-right:3px;text-align: center; " colspan="4"><div style="border-bottom: 1px solid #ddd; padding-bottom: 5px; ">numerical</div></th> </tr> <tr> <th style="text-align:right;font-style: italic;"> Sepal.Length </th> <th style="text-align:right;font-style: italic;"> Sepal.Width </th> <th style="text-align:right;font-style: italic;"> Petal.Length </th> <th style="text-align:right;font-style: italic;"> Petal.Width </th> <th style="text-align:left;font-style: italic;"> Species </th> </tr> </thead> <tbody> <tr> <td style="text-align:right;font-weight: bold;"> 5.1 </td> <td style="text-align:right;"> 3.5 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;font-weight: bold;"> 4.9 </td> <td style="text-align:right;"> 3.0 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;font-weight: bold;"> 4.7 </td> <td style="text-align:right;"> 3.2 </td> <td style="text-align:right;"> 1.3 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;font-weight: bold;"> 4.6 </td> <td style="text-align:right;"> 3.1 </td> <td style="text-align:right;"> 1.5 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;font-weight: bold;"> 5.0 </td> <td style="text-align:right;"> 3.6 </td> <td style="text-align:right;"> 1.4 </td> <td style="text-align:right;"> 0.2 </td> <td style="text-align:left;"> setosa </td> </tr> <tr> <td style="text-align:right;font-weight: bold;"> 5.4 </td> <td style="text-align:right;"> 3.9 </td> <td style="text-align:right;"> 1.7 </td> <td style="text-align:right;"> 0.4 </td> <td style="text-align:left;"> setosa </td> </tr> </tbody> </table> --- # Tables w/ `gt` <img src="scripts_output/sample_gt.png" width="2500" height="25%" style="display: block; margin: auto;" /> --- # DT and datatable ```r iris %>% head() %>% datatable(fillContainer=FALSE, options=list(pageLength=8)) ``` <div id="htmlwidget-81dc519e8d633ea35404" style="width:100%;height:auto;" class="datatables html-widget"></div> <script type="application/json" data-for="htmlwidget-81dc519e8d633ea35404">{"x":{"filter":"none","fillContainer":false,"data":[["1","2","3","4","5","6"],[5.1,4.9,4.7,4.6,5,5.4],[3.5,3,3.2,3.1,3.6,3.9],[1.4,1.4,1.3,1.5,1.4,1.7],[0.2,0.2,0.2,0.2,0.2,0.4],["setosa","setosa","setosa","setosa","setosa","setosa"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>Sepal.Length<\/th>\n <th>Sepal.Width<\/th>\n <th>Petal.Length<\/th>\n <th>Petal.Width<\/th>\n <th>Species<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"pageLength":8,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[8,10,25,50,100]}},"evals":[],"jsHooks":[]}</script> --- class: center, middle # Demo time! ## [Tables with `knitr`, `rmarkdown`, `DT`](scripts_output/tables_dt.html) ## [Tables with `GT`](scripts_output/tables_gt.html) --- # References - knitr: https://yihui.org/knitr/ - kableExtra: https://haozhu233.github.io/kableExtra/ - rmarkdown: https://rmarkdown.rstudio.com/ - DT: https://rstudio.github.io/DT/ - GT: https://gt.rstudio.com/index.html (cites other useful packages too) - Also checkout flextable: https://davidgohel.github.io/flextable/ --- class: center, middle, inverse # Thanks! <br> <br> #### How to reach me? ### Email: [janani@msu.edu](mailto:janani@msu.edu) ### Webpage: [jravilab.github.io](https://jravilab.github.io) ### Twitter: [@janani137](https://twitter.com/janani137) <br> <br> Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan) (Yihui Xie) and [R-Ladies theme](https://alison.rbind.io/project/rladies-xaringan/) (Allison Hill).