plot_evofreq: 'plot_evofreq' Plots the frequency dynamics using ggplot. Can...
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

Description Usage Arguments Value Examples

plot_evofreq Plots the frequency dynamics using ggplot. Can also use info to create animations

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plot_evofreq(freq_frame, n_time_pts = NULL, start_time = NULL,
  end_time = NULL, bw = 0.05, bc = "grey75", show_axes = TRUE,
  fill_range = NULL)

`freq_frame`	Proper dataframe returned by `get_evofreq`
`n_time_pts`	Integer defining how many time points to plot, evenly spaced between `start_time` and `end_time`. If NULL, all timepoints are plotted
`start_time`	Integer defining the timepoint at which to start plotting frequency dynamics. If NULL, plotting will begin at the first timepoint
`end_time`	Integer defining the timepoint at which to stop plotting frequency dynamics. If NULL, plotting will end at the last timepoint
`bw`	width of lines surrounding polygons
`bc`	color of lines surrounding polygons
`show_axes`	Whether to display axes
`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`.

ggplot of the frequency dynamics

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

#' 
### Setting of colors can be done when getting the freq_frame, or by updating the color later using \code{\link{update_colors}}. For a list of available colormaps, see https://github.com/bhaskarvk/colormap.
### Default colormap is rainbow_soft, but this can be changed using the \code{clone_cmap} argument. 
freq_frame <- get_evofreq(size_df, clones, parents)
evo_p <- plot_evofreq(freq_frame)

### Can color each clone by an attribute by providing a \code{fill_value}. Default colormap is viridis, but this can be changed using the \code{clone_cmap} argument
fitness <- runif(length(clones))
fitness_freq_frame <- get_evofreq(size_df, clones, parents, fill_value = fitness)
fitness_evo_p <- plot_evofreq(fitness_freq_frame)
#' 
### The user can also provide custom colors for each clone, which will need to be passed into the \code{fill_value} argument
### Custom colors can be defined using RGB values. Each color should be a string specifying the color channel values, separated by commas.
rgb_clone_colors <- sapply(seq(1, length(clones)), function(x){paste(sample(0:255,size=3,replace=TRUE),collapse=",")})
rgb_freq_frame <- get_evofreq(size_df, clones, parents, rgb_clone_colors)
rgb_evo_p <- plot_evofreq(rgb_freq_frame)

### Custom colors can also be any of the named colors in R. A list of the colors can be found with \code{colors()}
named_clone_colors <- sample(colors(), length(clones), replace = FALSE)
named_freq_frame <- update_colors(rgb_freq_frame, clones = clones, fill_value = named_clone_colors)
named_evo_p <- plot_evofreq(named_freq_frame)

### Custom colors can also be specified using hexcode
hex_clone_colors <- c("#614099ff", "#1d347eff", "#94558aff", "#c96872ff", "#f1884dff", "#e8fa5bff", "#042333ff","#f9bb41ff")
hex_freq_frame <- update_colors(rgb_freq_frame, clones = clones, fill_value = hex_clone_colors)
hex_evo_p <- plot_evofreq(hex_freq_frame)

### Can revert back to original colors
freq_frame_default_color <- update_colors(fitness_freq_frame, clones=clones)
default_cmap_evo_p <- plot_evofreq(freq_frame_default_color)

### Can add gganimate objects to evo_p_by_size to create the animation


library(gganimate)
movie_p <- fitness_evo_p +
  transition_reveal(x, range=range(fitness_freq_frame$x)) +
   view_follow()
# print(movie_p)
anim_save("evofreq_movie.gif", movie_p)