gGraph: gGraph

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

gGraph

Description

a genome graph object

Methods

Public methods

• gGraph$new()

• gGraph$walks()

• gGraph$set()

• gGraph$queryLookup()

• gGraph$disjoin()

• gGraph$simplify()

• gGraph$reduce()

• gGraph$subgraph()

• gGraph$clusters()

• gGraph$eclusters()

• gGraph$eclusters2()

• gGraph$paths()

• gGraph$dist()

• gGraph$rep()

• gGraph$swap()

• gGraph$connect()

• gGraph$toposort()

• gGraph$print()

• gGraph$annotate()

• gGraph$maxflow()

• gGraph$window()

• gGraph$gtrack()

• gGraph$trim()

• gGraph$fix()

• gGraph$add()

• gGraph$json()

• gGraph$get.diameter()

• gGraph$circos()

• gGraph$split()

• gGraph$clone()

---

Method new()

Usage

gGraph$new(
  genome = NULL,
  breaks = NULL,
  juncs = NULL,
  alignments = NULL,
  prego = NULL,
  jabba = NULL,
  cougar = NULL,
  weaver = NULL,
  remixt = NULL,
  rck = NULL,
  walks = NULL,
  nodes = NULL,
  edges = NULL,
  nodeObj = NULL,
  edgeObj = NULL,
  meta = NULL,
  verbose = FALSE
)

---

Method walks()

Usage

gGraph$walks(field = NULL, greedy = FALSE, verbose = FALSE)

---

Method set()

Usage

gGraph$set(...)

---

Method queryLookup()

Usage

gGraph$queryLookup(id)

---

Method disjoin()

Usage

gGraph$disjoin(
  gr = NULL,
  by = NULL,
  collapse = TRUE,
  na.rm = TRUE,
  avg = FALSE,
  sep = ",",
  FUN = default.agg.fun.generator(na.rm = na.rm, sep = sep, avg = avg)
)

---

Method simplify()

Usage

gGraph$simplify(
  by = private$pmeta$by,
  na.rm = TRUE,
  avg = TRUE,
  sep = ",",
  FUN = default.agg.fun.generator(na.rm = na.rm, sep = sep, avg = avg),
  ignore.loose = FALSE
)

---

Method reduce()

Usage

gGraph$reduce(...)

---

Method subgraph()

Usage

gGraph$subgraph(
  seed = si2gr(self),
  d = NULL,
  k = 0,
  bagel = FALSE,
  mod = FALSE,
  ignore.strand = T,
  verbose = FALSE
)

---

Method clusters()

Usage

gGraph$clusters(i = NULL, j = NULL, mode = "weak")

---

Method eclusters()

Usage

gGraph$eclusters(
  thresh = 1000,
  range = 1e+06,
  weak = TRUE,
  paths = !weak,
  mc.cores = 1,
  verbose = FALSE,
  chunksize = 1e+30,
  method = "single"
)

---

Method eclusters2()

Usage

gGraph$eclusters2(
  thresh = 1000,
  range = 1e+06,
  weak = TRUE,
  paths = !weak,
  mc.cores = 1,
  verbose = FALSE,
  chunksize = 1e+30,
  method = "single",
  return_pairs = FALSE,
  ignore.small = TRUE,
  max.small = 10000,
  ignore.isolated = TRUE,
  strict = c("strict", "one_to_one", "loose"),
  min.isolated = max.small,
  only_chains = FALSE
)

---

Method paths()

Usage

gGraph$paths(
  query,
  subject = query,
  mc.cores = 1,
  weight = NULL,
  meta = NULL,
  ignore.strand = TRUE,
  cartesian = TRUE
)

---

Method dist()

Usage

gGraph$dist(
  query,
  subject,
  weight = NULL,
  ignore.strand = TRUE,
  include.internal = TRUE,
  verbose = FALSE
)

---

Method rep()

Usage

gGraph$rep(nodes = NULL, times)

---

Method swap()

Usage

gGraph$swap(nodes, replacement)

---

Method connect()

Usage

gGraph$connect(
  n1,
  n2,
  n1.side = "right",
  n2.side = "left",
  type = "ALT",
  meta = NULL,
  insert = NULL
)

---

Method toposort()

Usage

gGraph$toposort()

---

Method print()

Usage

gGraph$print()

---

Method annotate()

Usage

gGraph$annotate(colName, data, id, class)

---

Method maxflow()

Usage

gGraph$maxflow(
  field = NA,
  walk = FALSE,
  max = TRUE,
  lower.bound = TRUE,
  nfield = NA,
  efield = NA,
  cfield = NA,
  path.only = TRUE,
  require.nodes = NULL,
  multi = FALSE,
  ncopies = 1,
  reverse.complement = FALSE,
  verbose = FALSE
)

---

Method window()

Usage

gGraph$window(pad = 0)

---

Method gtrack()

Usage

gGraph$gtrack(
  y.field = NULL,
  lwd.loose = 3,
  col.loose = alpha("blue", 0.6),
  col.alt = alpha("red", 0.4),
  ...
)

---

Method trim()

Usage

gGraph$trim(tile)

---

Method fix()

Usage

gGraph$fix(pattern = NULL, replacement = NULL, drop = TRUE, seqlengths = NULL)

---

Method add()

Usage

gGraph$add(nodes = NULL, edges = NULL, junctions = NULL)

---

Method json()

Usage

gGraph$json(
  filename = ".",
  maxcn = 100,
  maxweight = 100,
  save = TRUE,
  verbose = FALSE,
  annotations = NULL,
  nfields = NULL,
  efields = NULL,
  settings = list(y_axis = list(title = "copy number", visible = TRUE)),
  cid.field = NULL,
  no.y = FALSE
)

---

Method get.diameter()

Usage

gGraph$get.diameter(weights = NULL)

---

Method circos()

Usage

gGraph$circos(...)

---

Method split()

Usage

gGraph$split(by = "parent.graph")

---

Method clone()

The objects of this class are cloneable with this method.

Usage

gGraph$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.