I've tried to make this question clear and I'm sorry that I have not been able to provide an MRE as I wouldn't even know where to begin to make this a MRE, but let me know if you can identify an obvious issue?

In my R script when I run the graph and then click zoom, the following appears: Zoom correct graph

In markdown and also in the bottom right of plots (before clicking zoom), I get the following squashed and misformatted image

Let me know if you can help in any way and I'm sorry if this is not a well worded question.

I guess I want to know in short how to edit my markdown images to appear like they do when I click Zoom function. Sorry I'm pretty new to R and SO.