animate_evogram: animate_evogram View changes in the dendrogram over time. Has...
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

Description Usage Arguments Value Examples

animate_evogram

View changes in the dendrogram over time. Has most of the same options as plot_evogram, but does not have option to set link type

animate_evogram(size_df, clones, parents, fill_value = NULL,
  fill_range = NULL, time_pts = NULL, clone_cmap = NULL,
  threshold = 0.01, data_type = "size", fill_gaps_in_size = FALSE,
  test_links = TRUE, node_size = 5, scale_by_node_size = TRUE,
  orientation = "td", depth = "origin",
  rescale_after_thresholding = FALSE)

`size_df`	Dataframe in a wide format, where each row corrsponds to a single clone, and the columns are the sizes of that clone at each timepoint
`clones`	Array containing the clone ids. The index of each clone must correspond to the same index of the row in `size_df` that contains the sizes of that clone over time
`parents`	Array containing the ids of the parent of each clone in the `clones` array.
`fill_value`	Array containing information that can be used to color each clone. If NULL (the default), each clone is assigned a color. If values are a clone attribute, e.g. fitness, then the colors are assigned according to those values. The user can also provide custom colors in 3 ways: 1) hexcode; 2) rgb values as a string, with each value being a the intensity of the color channel, each separated by commas, e.g. "255, 10, 128"; 3) Any of the named in colors in R, which can be found with `colors`
`fill_range`	Array containing the minimum and maximum values to set the range of colors. If NULL (the default), the range is determined directly from `fill_value`.
`time_pts`	Array containing the name of the timepoints. If NULL, then the name of timepoints will be a sequence from 1 to the number of columns in `size_df`.
`clone_cmap`	Colormap to use for the clones. For a list of available colormaps, see https://github.com/bhaskarvk/colormap.
`threshold`	The minimum frequency of clones to be plotted. Clones with with a frequency below this value will not be plotted
`data_type`	String defining what kind of information is in size_df. If "size", then the values in `size_df` are the population sizes. If "mutation", the values are the frequencies, between 0 and 1, of each mutation in the population over time
`fill_gaps_in_size`	Boolean defining whether or not missing sizes should be filled in
`test_links`	Make sure clone does not have the same id as it's parent. If true, it can cause infinite recursion.
`node_size`	Determines the size of nodes if `scale_by_node_size` is FALSE
`scale_by_node_size`	Boolean defining if the size of each node should be proportional to its frequency. If FALSE, then all nodes have the same size, determined by `node_size`
`orientation`	Defines orientation of the tree: "td" draws it top-down, "lr" draws it left-right
`depth`	Determines the y-position of the nodes: "level" places the nodes based on how deeply they are nested in the tree, "origin" makes the y-position the same as the clone's origin time, "bottom" positions nodes so that all leaves have the same position, furthest from the root
`rescale_after_thresholding`	Boolean determining if frequencies should be rescaled after thresholding, so that frequencies are based on what was above the threshold.

List infromation need to craete the animation: "dendro_pos_df" contains all of the positions of the nodes and edges at each timestep, while "animation_plot" that can be used with gganimate to create the animation. For details on how to customize and save the animation, see gganimate

data("example.easy.wide.with.attributes")
### Split dataframe into clone info and size info using fact timepoint column names can be converted to numeric values
time_col_idx <- suppressWarnings(which(! is.na(as.numeric(colnames(example.easy.wide.with.attributes)))))
attribute_col_idx <- suppressWarnings(which(is.na(as.numeric(colnames(example.easy.wide.with.attributes)))))
size_df <- example.easy.wide.with.attributes[, time_col_idx]
parents <- example.easy.wide.with.attributes$parent
clones <- example.easy.wide.with.attributes$clone
fitness <- example.easy.wide.with.attributes$fitness
dendro_movie_info <- animate_evogram(size_df, clones = clones, parents = parents, fill_value = fitness)
dendro_movie_plot <- dendro_movie_info$animation_plot

### Add gganimate object to dendro_movie_plot to finish animation

library(gganimate)
movie_p <- dendro_movie_plot +
  transition_time(time) +
  ease_aes() +
  exit_shrink() +
  ggtitle('Time {frame_time}')

print(movie_p)