iGraph figures chopped off in R markdown - r

Question

I have some code that generates layouts for the following minimum spanning tree "cell_dtree":
> cell_dtree
IGRAPH 951dfd5 D--- 720 719 --
+ edges from 951dfd5:
[1] 400-> 1 1-> 2 38-> 3 3-> 4 197-> 5 10-> 6 10-> 7 13-> 8 1-> 9 28-> 10 225-> 11 362-> 12 30-> 13
[14] 20-> 14 148-> 15 3-> 16 13-> 17 160-> 18 435-> 19 1-> 20 60-> 21 38-> 22 9-> 23 68-> 24 9-> 25 178-> 26
[27] 21-> 27 1-> 28 60-> 29 2-> 30 1-> 31 2-> 32 1-> 33 352-> 34 21-> 35 20-> 36 1-> 37 1-> 38 554-> 39
[40] 3-> 40 554-> 41 333-> 42 352-> 43 126-> 44 1-> 45 69-> 46 227-> 47 160-> 48 1-> 49 1-> 50 37-> 51 708-> 52
[53] 705-> 53 185-> 54 307-> 55 48-> 56 667-> 57 563-> 58 428-> 59 519-> 60 428-> 61 707-> 62 1-> 63 707-> 64 707-> 65
[66] 707-> 66 214-> 67 20-> 68 68-> 69 37-> 70 453-> 71 57-> 72 148-> 73 345-> 74 69-> 75 148-> 76 80-> 77 79-> 78
[79] 9-> 79 70-> 80 68-> 81 148-> 82 23-> 83 345-> 84 454-> 85 345-> 86 36-> 87 345-> 88 36-> 89 311-> 90 148-> 91
[92] 13-> 92 345-> 93 13-> 94 350-> 95 326-> 96 79-> 97 666-> 98 539-> 99 430->100 554->101 213->102 20->103 38->104
[105] 21->105 172->106 112->107 1->108 20->109 453->110 80->111 703->112 20->113 9->114 79->115 1->116 47->117
+ ... omitted several edges
Here is the r markdown code to create the plot.
```{r, results='asis', fig.width = 7, fig.heigt = 7}
set.seed(1)
l2 <- igraph::layout.lgl(cell_dtree)
l2 <- igraph::layout.norm(l2, ymin = -2, ymax = 2, xmin = -2, xmax = 2)
plot(cell_dtree,
rescale = F,
layout = l2 * 1,
edge.arrow.width=0.1,
vertex.label=NA,
vertex.size=1,
vertex.label=NA,
edge.width=0.5,
edge.arrow.size=0.5,
edge.arrow.width=0.7)
```
When this document goes through knittr, the plot looks like it has been cut off, only a rectangular region in the center is displayed in the knitr html output.
To troubleshoot the issue, I ran igraph's implementation of Erdos-Renyi graph, using the same number of vertices (720) as the graph above, and the same plotting parameters:
```{r, results='asis', out.width = '100%', out.height = '100%', fig.width = 7, fig.heigt = 7}
er <- igraph::sample_gnm(n=720, m=40)
plot(er, vertex.size=6, vertex.label=NA)
set.seed(1)
l2 <- igraph::layout.lgl(er)
l2 <- igraph::layout.norm(l2, ymin = -2, ymax = 2, xmin = -2, xmax = 2)
plot(er,
rescale = F,
layout = l2 * 1,
vertex.label=NA,
vertex.size=1,
vertex.label=NA,
edge.width=0.5,
edge.arrow.size=0.5,
edge.arrow.width=0.7)
```
However, the resulting image does exactly what I want it to do: fill the figure box in an efficient way without those big white borders. Obviously not all the vertices are displayed here, but the scaling helps to show that the layout is using all available space for the image: