mpra_tile_plot: Make a MPRA tile plot
In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Make a tile plot of the MPRA counts for a given variant

mpra_tile_plot(
  variant_id,
  variant_counts,
  show_barcodes = FALSE,
  composite = FALSE,
  sampler_res = NULL,
  prob = 0.5,
  prob_outer = 0.95
)

`variant_id`	variant ID
`variant_counts`	a data frame of counts for one variant
`show_barcodes`	a logical indicating whether to show the barcodes on the left side of the tile plot
`composite`	a logicial indicating whether or not to include the extra plot components on the right sides
`sampler_res`	A stanfit object for one variant
`prob`	if composite = TRUE, a fraction between 0 and 1 indicating the posterior probability mass to include in the inner intervals.
`prob_outer`	if composite = TRUE, a fraction between 0 and 1 indicating the posterior probability mass to include in the outer intervals.

The barcodes in the output tile plot are sorted according the their average DNA representation.

The barcodes in variant_counts need to be in the same order that they were presented to the malacoda sampler. malacoda tries to preserve the ordering present in the original mpra_data dataset (not including removed poorly represented barcodes), but if you're unsure you can pull from the variant_data column in the analysis_res object. Currently it's necessary that the allele be encoded by 'alt' and 'ref'.

Setting composite = TRUE will include three additional components: a column of tiles whose color indicates the log(mean(RNA)/ mean(DNA)) by row, and posterior interval plots for the variant's activities and transcription shift.

andrewGhazi/malacoda documentation built on Aug. 2, 2020, 12:54 a.m.