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Build Grammateus plot specs for nanopore QC report families

Source: R/qc_plots.R
qc_plot_yield_over_time.Rd

These helpers convert floundeR QC tables and curated Bamana/POD5 summary objects into backend-neutral Grammateus ReportPlot specifications. They do not render plots directly and do not require private Grammateus runtime assets.

Usage

qc_plot_yield_over_time(
  x,
  y = c("cumulative_bases", "cumulative_read_count"),
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_quality_distribution(
  x,
  y = c("read_count", "bases"),
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_read_length_distribution(
  x,
  y = c("read_count", "bases"),
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_flowcell_density(
  x,
  y = c("bases", "read_count", "pass_fraction"),
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_barcode_balance(
  x,
  y = c("read_fraction", "bases_fraction", "read_count", "bases"),
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_pod5_integrity(
  x,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_bam_mapping_summary(
  x,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_bam_mapq_distribution(
  x,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

qc_plot_bam_flag_summary(
  x,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL,
  output = NULL
)

Arguments

x

A floundeR QC table, POD5 evidence table, or bam_summary() result appropriate for the plot family.

y

Metric to plot where the plot family supports alternatives.

produced_by

Producing software or service name.

producer_version

Producing software version.

produced_at_utc

Production timestamp.

run_id

Optional upstream run, workflow, or analysis identifier.

output

Grammateus plot output definition.

Value

A flounder_grammateus_plot_spec object.