Struct CellRules 

pub struct CellRules { /* private fields */ }

Cell QC as rules, with what each does.

Implementations

impl CellRules

pub fn new(metrics: QcMetrics, cfg: QcConfig) -> Self

Rules over metrics (with its per-gene cell counts measured) under cfg. The histogram printing of cfg is left to compute_qc.

pub fn metrics(&self) -> &QcMetrics

pub fn config(&self) -> &QcConfig

pub fn rules(&self) -> &[Rule]

The rules the data has, in table order.

pub fn verdicts(&self) -> &Verdicts

The verdicts under the current settings.

pub fn count(&self, rule: Rule) -> &RuleCount

What rule does now.

pub fn removed(&self, rule: Rule) -> &[bool]

Whether each cell (each gene, for Rule::GeneCells) is removed now.

pub fn band(&self, rule: Rule) -> Option<RobustBand>

The robust band of rule’s metric on its own scale, as qc_lib fits it (over the cells above the near-empty floor), whether or not the rule holds to it; None for a rule with no band, or no spread.

pub fn kept_cells(&self) -> Vec<usize>

The cells QC keeps (in the output), and how many there are.

pub fn kept_genes(&self) -> Vec<usize>

The genes QC keeps.

pub fn values(&self, rule: Rule) -> &[f32]

The values rule is held to: one per cell, or per gene.

pub fn is_on(&self, rule: Rule) -> bool

Whether rule decides anything now.

pub fn mode(&self, rule: Rule) -> Mode

How rule’s edge is set now.

pub fn banded(rule: Rule) -> bool

Whether rule can be set by the MAD band.

pub fn edge(&self, rule: Rule) -> Option<f32>

The edge rule holds its metric to now, on the metric’s own scale: the tightest of its band edge and its own value; None when it is off or its band has no spread.

pub fn set_on(&mut self, rule: Rule, on: bool)

Turn rule off, or back on as the starting settings had it (by the MAD band where it has one; a cap where it has none, at the largest value, keeping everything until it is moved).

pub fn set_value(&mut self, rule: Rule, value: f32)

Hold rule to value of its own, off the MAD band.

pub fn set_mads(&mut self, n_mads: f32)

Set the MAD band’s width, which every banded rule shares.

pub fn toggle_mode(&mut self, rule: Rule)

Switch rule between the MAD band and a value of its own, the value starting where the edge is now. Back on the band, its own value returns to the starting one.

pub fn reset(&mut self)

Back to the starting settings.

pub fn overlap(&self) -> &[(Vec<Rule>, usize)]

The removed cells grouped by the cell rules each fails on its own, largest group first. A cell removed only as the rules act together (a band refitted without a floor, say) has an empty set.

pub fn flags(&self) -> Vec<String>

qc flags that decide what these settings do, past qc’s defaults. The mito pattern is always given, an empty one turning the metric off (qc starts from a pattern of its own); under --qc-auto-cutoff the gene rule is always given too, 0 for off, as qc puts it at the trough only when none is given.