read.HAL: read.HAL
In MathOnco/EvoFreq: Clonal Dynamic Visualizations

Description Usage Arguments Value Examples

read.HAL

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read.HAL(path_to_file, fill_name = NULL, get_evofreq_df = TRUE,
  get_evofreq_arg_list = list(), get_dendogram_df = FALSE,
  get_evogram_arg_list = list())

`path_to_file`	String defining the location of the data output from HAL
`fill_name`	Optional string defining which attribute to color by. See `update_colors` for more details.
`get_evofreq_df`	Boolean defining if a freq_frame and evofreq should be returned.
`get_evofreq_arg_list`	List containing additional arguments passed to `get_evofreq`
`get_dendogram_df`	Boolean defining if the dataframes to plot evograms and the evogram itself should be returned.
`get_evogram_arg_list`	List containing additional arguments passed to `get_evogram`

List containing information get and plot Muller plots and dendrograms

## Default is to return the plot and all info needed to create new ones
hal_info <- read.HAL(path_to_hal_results)
print(hal_info$evofreq_plot)

### Can define column to use for coloring
hal_info <- read.HAL(path_to_hal_results, fill_name = "Passengers")
print(hal_info$evofreq_plot)

### The information needed to create new plots is also returned. This can be useful if you want to change colors
updated_plot <- update_colors(hal_info$freq_frame, hal_info$clones, hal_info$attributes$Drivers)
plot_evofreq(updated_plot)

### Can use a list to pass additional arguments to get_evofreq
evofreq_args <- list("threshold"=0.0, "clone_cmap"="plasma")
hal_info <- read.HAL(path_to_hal_results, fill_name = "Passengers", get_evofreq_arg_list = evofreq_args)
print(hal_info$evofreq_plot)

### Use the same approach to get dendrograms by setting  get_dendogram_df = T.  Set return_dendrogram_plot = T to get the dendrogram plot too
evogram_args <- list("threshold"=0.0, "clone_cmap"="plasma")
hal_info <- read.HAL(path_to_hal_results, fill_name = "Drivers", get_evogram_arg_list = evofreq_args, get_dendogram_df=T)
print(hal_info$evogram_plot)