Process sashimi plot input into standardized data frames

This function converts coverage and junction inputs of various types into standardized data frames for sashimi plot visualization. It supports the same input types as process_signal_input for coverage data (GRanges, data.frame, character vector of file paths, or named list), and processes junction data in parallel.

Usage

process_sashimi_input(
  coverage_data,
  junction_data,
  region,
  track_labels = NULL,
  junction_direction = c("alternate", "up", "down")
)

Arguments

coverage_data

A GRanges object, data frame, character vector of file paths, or named list. Same input types supported as ez_coverage.

junction_data

Junction input that must match the structure of coverage_data:

• If coverage_data is a single source (GRanges, data.frame, or single file path), junction_data must also be a single source.

• If coverage_data is a named list, junction_data must be a named list with the same names.

region

A genomic region string in the format "chr:start-end"

track_labels

Optional vector of track labels (used for character vector input)

junction_direction

Direction of junction arcs: "alternate" (default), "up", or "down"

Value

A list with two data frames: coverage_df and junction_df, both with a 'track' column when input is a list. junction_df has additional columns: y_start, y_end, arc_direction, start1, start2

Examples

if (FALSE) { # \dontrun{
# Single data frame input
coverage <- data.frame(seqnames = "chr1", start = 1:100, end = 2:101, score = runif(100))
junctions <- data.frame(seqnames = "chr1", start = c(20, 60), end = c(40, 80), score = c(5, 10))
result <- process_sashimi_input(coverage, junctions, "chr1:1-100")

# Named list input (multiple tracks)
cov_list <- list("Sample1" = cov_df1, "Sample2" = cov_df2)
junc_list <- list("Sample1" = junc_df1, "Sample2" = junc_df2)
result <- process_sashimi_input(cov_list, junc_list, "chr1:1-100")
} # }