PewitR6: Pewit R6 Class

In iferres/pewit: Microbial Pan-Genomics in R

Pewit R6 Class

Description

Pewit R6 Class

Pewit R6 Class

Super classes

pagoo::PgR6 -> pagoo::PgR6M -> pagoo::PgR6MS -> PewitR6

Methods

Public methods

• PewitR6$new()

• PewitR6$gene_context()

• PewitR6$gg_gene_context()

• PewitR6$clone()

Inherited methods

• pagoo::PgR6$add_metadata()
• pagoo::PgR6$drop()
• pagoo::PgR6$recover()
• pagoo::PgR6$save_pangenomeRDS()
• pagoo::PgR6$write_pangenome()
• pagoo::PgR6M$cg_exp_decay_fit()
• pagoo::PgR6M$dist()
• pagoo::PgR6M$gg_barplot()
• pagoo::PgR6M$gg_binmap()
• pagoo::PgR6M$gg_curves()
• pagoo::PgR6M$gg_dist()
• pagoo::PgR6M$gg_pca()
• pagoo::PgR6M$gg_pie()
• pagoo::PgR6M$pan_pca()
• pagoo::PgR6M$pg_power_law_fit()
• pagoo::PgR6M$rarefact()
• pagoo::PgR6M$runShinyApp()
• pagoo::PgR6MS$core_seqs_4_phylo()

---

Method new()

Usage

PewitR6$new(
  data,
  org_meta,
  cluster_meta,
  core_level = 95,
  sep = "__",
  sequences,
  verbose = TRUE
)

---

Method gene_context()

Usage

PewitR6$gene_context(cluster, upstream = 2, downstream = 2)

---

Method gg_gene_context()

Usage

PewitR6$gg_gene_context(
  cluster,
  upstream = 2,
  downstream = 2,
  fill = "cluster",
  orient = TRUE
)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

PewitR6$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

iferres/pewit documentation built on June 22, 2022, 8:34 p.m.