Description Usage Arguments Details
Make a tile plot of the MPRA counts for a given variant
1 2 3 4 5 6 7 8 9 | 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.
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