Description Usage Arguments Value Examples
A function to plot a MuHiSSE (model-averaged) marginal ancestral reconstruction for the trait data.
1 2 3 4 5 6 7 8 9 10 11 12 | m_trait_recon_cp(
processed_recon,
show_tip_labels = FALSE,
tree_layout = "rectangular",
tree_direction = "right",
time_axis_ticks = 10,
open_angle = 10,
focal_character = c("prob_0x", "prob_x0"),
focal_character_label,
second_character_label,
colors = viridis(9)[c(5, 1, 9)]
)
|
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 |
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). Passed on to |
open_angle |
The degrees of empty space between the first and last tip. Only works for |
focal_character |
Specifies the x axis of the two-dimensional color key. Either |
focal_character_label |
Label for the x axis of the two-dimensional color gradient. This should match the focal probability. |
second_character_label |
Label for the y axis of the two-dimensional color gradient. |
colors |
A vector of three colors in the order: (1) zero color (color when the two traits are in state 0), (2) horizontal_color (color to interpolate towards state 1 of the focal character) and (2) vertical_color (color to interpolate towards state 1 of the second character). See |
A plot of the phylogeny with branches colored by muhisse-inferred marginal ancestral states.
1 2 3 4 5 6 7 8 9 10 11 12 | library("colorplaner")
data("diatoms")
processed_muhisse <- m_process_recon(muhisse_recon=diatoms$muhisse_recon)
m_trait_recon_cp(
processed_recon = processed_muhisse,
tree_layout = "fan",
focal_character = "prob_0x",
focal_character_label = "p(marine)",
second_character_label = "p(plankton)",
colors = c("#21908CFF", "#440154FF", "#FDE725FF")
)
|
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