update_colors: update_colors Update the colors of clones in the frequency...
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

update_colors

Update the colors of clones in the frequency dynamics dataframe or dendrogram plot dataframe

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update_colors(evo_freq_df, clones, fill_value = NULL,
  clone_cmap = NULL, fill_range = NULL, fill_name = NULL,
  shuffle_colors = FALSE)

`evo_freq_df`	Dataframe returned by `get_evofreq` or `get_evogram` , which contains the information to plot the frequency dynamics
`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
`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`
`clone_cmap`	String defining which colormap should be used to color the clones (nodes) if no attributes to color by. For a list of available colormaps, see https://github.com/bhaskarvk/colormap
`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`.
`fill_name`	String defining the name of the attribute used for coloring. If NULL, the default, the name will be inferred from the `fill_value` argument.
`shuffle_colors`	Boolean determining if colors should be shuffled before being assigned to each clone. Only applies when fill_value = NULL

data("example.easy.wide")
### 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)))))
size_df <- example.easy.wide[, time_col_idx]
parents <- example.easy.wide$parents
clones <- example.easy.wide$clones
### 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. There is also the option to set the color range using the \code{fill_range} argument
fitness <- runif(length(clones),0, 100)
fitness_freq_frame <- update_colors(freq_frame, clones = clones, fill_value = fitness, fill_range= c(0, 100))
fitness_evo_p <- plot_evofreq(fitness_freq_frame,  fill_range = c(0, 100))

### 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 <- update_colors(freq_frame, clones = clones, fill_value = 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(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(freq_frame, clones = clones, fill_value = hex_clone_colors)
hex_evo_p <- plot_evofreq(hex_freq_frame)

### Method can also be used to update node colors of the dendrograms
dendro_df <- get_evogram(size_df, clones, parents)
tree_pos <- dendro_df$dendro_pos
tree_links <- dendro_df$links
tree_p <- plot_evogram(tree_pos, tree_links)

### Color node by fitness
tree_pos_fitness_color <- update_colors(evo_freq_df = tree_pos, clones = clones, fill_value = fitness)
tree_p_fitness <- plot_evogram(tree_pos_fitness_color, tree_links)
### Color node using custom colors in hexcode format
tree_info_custom_color <- update_colors(evo_freq_df = tree_pos, clones = clones, fill_value = hex_clone_colors)
tree_p_custom_color <- plot_evogram(tree_info_custom_color, tree_links)