Even though I have been using RStudio since it's release, it's only been recently that I've explored changing the default pane layout. I've seen a lot of screenshots in the wild with the console and source panes on separate sides and now I've become a big fan of that layout. Anyone else want to share their preferred layout and other tweaks that optimize your 
RStudio sessions?
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I'm one of those people with my panes set up how you mentioned. It makes it so much easier to work with my console and source code at the same time. if you use .RMD a lot it'll help to download the R addin remedy. Which makes typing markdown a lot easier. I've also mapped the knit command to a button on my mouse so I can knit documents when I need to use the mouse.
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My layout can be seen above. I use:
Rstudio Theme: Modern
Editor Theme: Cobalt
Zoom: 150% (on a ~24" screen @ 4k)
Font: InputMono Light / 10
In the past, I have used a second screen in portrait mode for the console, but my desk does not have the room. Keeping it and the editor separate is advantageous.
Pop-out frames can be great too, especially for plots.
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I don't change the theme but I do keep a console-script-plots-environment [clockwise from top left] order. I also really enjoy keeping a visible line at the 80 character mark in my script, to keep readability in mind when writing long things.
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I have the source pane top left, but I make it full screen. Below it, minimized, is history and viewer. Top right is console, bottom right is everything else.
I primarily work on a widescreen 27" display, so vertical space is a premium and horizontal space is plentiful. I'd really like more flexibility in pane layout. Ideally a three column layout with source and console taking one column each, and everything else taking the last column.
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My pane layout. But for classes I change them to the standard, that my students may not get confused.
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My 
to everyone for sharing their RStudio setups! This gives me a lot of ideas to try. I often view the help tab in full vertical space especially when writing packages so I like having both that and the files fully stretched out. And tearing selected files out to my second monitor makes it a lot easier especially when developing shiny apps.
Interesting. But i can't build this one. When select only "files" alone, it goes to the standard =(
Strange... Looks like a bug worth the separate issue.
You say I should open a discussion?
I haven't search much about it. And true, sometimes I have some problems with this part of RStudio... But I'm sure it could help somebody, if you'll describe your problem in different topic, printscreening every step.
I like having a large plot panel so I basically put History,Connections and Packages on the RHS bottom and hide that part, so half of my screen is Environment/Files/Plots/Help/VCS and Viewer. I keep the LHS untouched, with the script at the top and the console at the bottom.
But I came here because I was looking for a solution because recently the layout keeps resetting itself. Have you found the same problem? Should I post a new topic about this?
Edit: a quick update if you are here because of pane layout problems, this has been discussed in Windows Pane Layout Breaks Under Certain Combinations (I couldn't find it because I was looking for "paneL layout" instead of "pane layout").
I've tried various layouts but the one I have currently works quite well for the thing I am working on:
- I have a RMarkdown document I am editing. I pop this out into its own window, full-height to my screen and 80 columns wide (plus I have the document outline sidebar open).
- I then have the plot/view zoom in its own square window, not too big.
- Then I have the main RStudio window open but quite small, with Console zoomed (Ctrl+Shift+2) so that's all I see of that window
Mostly I am working in the RMarkdown editor window and using Ctrl+Enter/Ctrl+Shift+Enter to run lines or chunks, which then execute in the Console window. Ctrl+2 takes my focus over to the Console. Alt+Tab takes me back to the editor. Ctrl+Shift+5 takes me to the files pane zoomed in, Ctrl+Shift+8 takes me to the Environment tab. Other shortcuts open other panes but I rarely use most of the other panes at the moment.
My main frustration is that when I generate a new plot, it doesn't just render in the zoomed viewer window but also in the Viewer tab, which takes focus away from the console, so then I have to do Ctrl+2 to get the focus back to the console. If I could turn this behaviour off then I would be very happy.