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List All Cells in Gradient Flow Result

Source: R/gfc_flow.R
list.cells.gfc.flow.Rd

Enumerates all cells (min-max pairs) in a gfc.flow result, including cells with spurious endpoints (unless excluded). Optionally augments each cell with binary outcome counts over unique cell vertices.

Usage

# S3 method for class 'gfc.flow'
list.cells(
  x,
  include.spurious = TRUE,
  loc.min = NULL,
  loc.max = NULL,
  include.spurious.flags = FALSE,
  y = NULL,
  include.max.label = FALSE,
  include.min.vertex = FALSE,
  include.max.vertex = FALSE,
  ...
)

Arguments

x

A gfc.flow object from compute.gfc.flow().

include.spurious

Logical; if TRUE (default), include cells with spurious endpoints.

loc.min

Optional. If non-NULL, filter to cells with this minimum endpoint. Can be a vertex index (numeric/integer) or a label (character).

loc.max

Optional. If non-NULL, filter to cells with this maximum endpoint. Can be a vertex index (numeric/integer) or a label (character).

include.spurious.flags

Logical; if TRUE, include logical columns min.is.spurious and max.is.spurious in the returned data frame. Default FALSE.

y

Optional. A binary outcome vector of length x$n.vertices (or length equal to the number of vertices). Must be coded as 0/1 or logical. If provided, adds columns "n(y = 1)", "n(y = 0)", "ratio", "rel.ratio" computed over unique cell vertices.

include.max.label

Logical; if TRUE include max.label column. Default FALSE.

include.min.vertex

Logical; if TRUE include min.vertex column. Default FALSE.

include.max.vertex

Logical; if TRUE include max.vertex column. Default FALSE.

...

Extra parameters.

Value

A data frame with (always) columns:

min.label

Minimum label.

n.trajectories

Number of trajectories connecting this pair.

unique.vertices

Number of unique vertices in trajectories.

Optionally includes endpoint columns depending on flags:

max.label

Maximum label (if include.max.label = TRUE).

min.vertex

Minimum vertex index (if include.min.vertex = TRUE).

max.vertex

Maximum vertex index (if include.max.vertex = TRUE).

If include.spurious.flags = TRUE, also includes:

min.is.spurious

TRUE if the minimum endpoint is spurious.

max.is.spurious

TRUE if the maximum endpoint is spurious.

If y is provided, also includes:

n(y = 1)

Count of outcome==1 among unique cell vertices.

n(y = 0)

Count of outcome==0 among unique cell vertices.

ratio

n(y=1) / (n(y=0)+n(y=1)).

rel.ratio

ratio / mean(y) (global prevalence).