Description Usage Arguments Value Examples
A function to plot a (model-averaged) marginal ancestral reconstruction for the trait data.
1 2 3 4 5 6 7 8 9 10 11 12 13 |
processed_recon |
An object produced by |
show_tip_labels |
Logical, whether to plot tip labels. Default is FALSE because it is difficult to plot legible tip labels for larger trees common in this type of analysis. See |
trait_name |
The name of the trait to be used for guide title |
states_names |
The names for character states |
colors |
Colors for the two character states. If |
discrete |
Logical. Whether to discretize the probabilities of ancestral states into binary (0/1) |
cutoff |
A decimal to be used as a threshold for discretizing |
tree_layout |
A layout for the tree. Available options are 'rectangular' (default), 'slanted', 'circular', 'fan' and 'radial'. |
tree_direction |
'right' (default), 'left', 'up', or 'down' for rectangular and slanted tree layouts |
time_axis_ticks |
numeric giving the number of ticks for the time axis (default=10) |
open_angle |
The degrees of empty space between the first and last tip. Only works for |
A plot of the phylogeny with branches colored by hisse-inferred marginal ancestral states.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | data("diatoms")
processed_hisse <- h_process_recon(hisse_recon=diatoms$cid4_recon)
map_continuous <-
h_trait_recon(
processed_recon = processed_hisse,
trait_name = "", discrete=FALSE, cutoff=.5)
# change colors, your can pass the trait name to `name=` to title the colorbar
map_continuous + scale_color_gradient(name="", low = "#132B43", high = "#56B1F7")
map_discrete <-
h_trait_recon(
processed_recon = processed_hisse,
trait_name = "", discrete=TRUE, cutoff=.5)
# change colors
map_discrete + scale_color_manual(name="", values = c("red", "blue"))
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