Calculate PGA per chromosome; updates to prettyRainfallPlot

[kmcoyle]

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#' @title ASHM Rainbow Plot
#'
#' @description Make a rainbow plot of all mutations in a region, ordered and coloured by metadata.
#'
#' @details This function creates a rainbow plot for all mutations in a region. Region can either be specified with the `region` parameter,
#' or the user can provide a maf that has already been subset to the region(s) of interest with `mutation_maf`.
#' As a third alternative, the regions can also be specified as a bed file with `bed`.
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#'
#' @param mutations_maf A data frame containing mutations (MAF format) within a region of interest (i.e. use the get_ssm_by_region).
#' @param metadata should be a data frame with sample_id as a column.
#' @param exclude_classifications Optional argument for excluding specific classifications from a metadeta file.
#' @param drop_unmutated Boolean argument for removing unmutated sample ids in mutated cases.
#' @param classification_column The name of the metadata column to use for ordering and colouring samples.
#' @param bed Optional data frame specifying the regions to annotate (required columns: start, end, name).
#' @param region Genomic region for plotting in bed format.
#' @param custom_colours Provide named vector (or named list of vectors) containing custom annotation colours if you do not want to use standartized pallette.
#' @param hide_ids Boolean argument, if TRUE, ids will be removed.
#'
#' @return ggplot2 object.
#'
#' @import dplyr ggplot2
#' @export
#'
#' @examples
#' #basic usage
#' region = "chr6:90975034-91066134"
#' metadata = get_gambl_metadata()
#' plot = ashm_rainbow_plot(metadata = metadata, region = region)
#'
#' #advanced usages
#' mybed = data.frame(start = c(128806578,
#'                              128805652,
#'                              128748315),
#'                    end = c(128806992,
#'                            128809822,
#'                            128748880),
#'                    name = c("TSS",
#'                             "enhancer",
#'                             "MYC-e1"))
#'
#' ashm_rainbow_plot(mutations_maf = my_mutations,
#'                   metadata = my_metadata,
#'                   bed = mybed)
#'

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[Kdreval]

I think this is fine to leave like this but when migrating to the child repo I will change this to directly pull from the chr_coordinates object defined just before this 😄

[kmcoyle]

seems fine to me!

[Kdreval]

This can probably be an argument in the collate_pga? I think it is fine to keep as is but I can incorporate this into that function when migrating. What do you think?

[kmcoyle]

That would work; I think I had a separate collate function elsewhere but inside pga would be most convenient.

[Kdreval]

I trust this works for the chr-prefixed too?

[kmcoyle]

good catch, should probably change to
sv_chromosome = standardize_chr_prefix(incoming_vector = c(1:22,"X","Y"), projection = projection)

[Kdreval]

Nice trick with expression!

[Kdreval]

Thanks for the update! I will merge this and then will transfer the updates to the appropriate child, while also modifying some small things!

[Kdreval]

The updates introduced in this PR are now migrated to the appropriate children repos:

• prettyRainfallPlot() is in GAMBLR.viz (#30)
• calculate_pga_chr() is an optional argument per_chromosome in calculate_pga() of GAMBLR.utils (#27)
• collate_pga_chr() is also an optional argument per_chromosome in collate_pga() of GAMBLR.results (#22)