Friday, April 13, 2018

Some new features to modernize plotTree.wBars

After posting a recent hack demonstrating how to plot stacked bars on a fan tree using plotTree.wBars in phytools I decided it might be useful to modernize the function a bit.

One feature I though I could add was dotted linking lines leading from the tip of the tree to either the tip label or the bar for non-ulrametric trees. The reason for this is because it can be very difficult to line-up the bar with its corresponding tip if the some tips terminate before the present.

Another feature that I thought I'd get rid of at the same time is the fact that for all x > 0 the behavior of the function is to attach the bars directly to the tip - regardless of whether or not it terminates in the present.

Here's what I mean:


plot of chunk unnamed-chunk-1



plot of chunk unnamed-chunk-2

Obviously this could be undesirable under some circumstances.

Note that the function does not behave this way when some or all values of x are negative:


plot of chunk unnamed-chunk-3

Let's load the update version from GitHub & see how it compares. Note that we would normally just update phytools from GitHub using devtools.


plot of chunk unnamed-chunk-4

## or

plot of chunk unnamed-chunk-4

## and

plot of chunk unnamed-chunk-4

Note that the default scale is different. The old version used an ignorant scale which could result in some pretty ludicrous plots by default. This should be better.


  1. Richard R. Cole Is expert of outdoor tools and gadgets to aid you in selecting appropriate product among thousands of options

  2. swiss replica watches sale , combining elegant style and cutting-edge technology, a variety of styles of rolex datejust replica, the pointer walks between your exclusive taste style.

  3. A month later, the two returned to the bride's hometown to have a
    rolex replica watches . Beatrice wore Giorgio Armani Prive's custom-made ivory
    white silk wedding replica watches , elegant and noble.