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When Markdown (and RMarkdown) print a value, they put the value in a <pre> tag and use the R value printer, which puts a ## before the value. This might be what you want when outputting numerical values, but it looks pretty ugly when printing an interactive plot.
Use
```{r results='asis'}
to print the value without this (anti-)formatting.
Set the fonts/size?
Inject custom css rules using rcloud.install.css, passing the URI to a CSS asset in your notebook, e.g.
This must be after the rcloud.dcplot library is loaded with require or library.
Take a look at dc.css (or use the elements browser of your browser) to see what is customizable. Your rules need to be at least as specific as the rules in dc.css.
Change the placement/layout of the charts in the page?
dc.js adds the class dc-chart to the element you pass as the root. Then it sets float: left in dc.css. Override this in your custom CSS as described above.