mmnetwork: Network plot of mate-pair or paired-end connected scaffold...
In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description Usage Arguments Value Using the locator with mmnetwork Author(s) Examples

Plots all connected scaffolds in a network plot. Scaffolds can then be highlighted and extracted using the locator and selection features.

mmnetwork(
  mm,
  network,
  min_connections = 1,
  color_by = NULL,
  color_scale_log10 = FALSE,
  locator = FALSE,
  selection = NULL,
  highlight_labels = NULL,
  highlight_color = "darkred",
  links_scale = 1,
  scaffold_labels = FALSE,
  print_nolinks = FALSE,
  seed = 0
)

`mm`	(required) A dataframe loaded with `mmload`.
`network`	(required) Paired-end or mate-pair connections between scaffolds in long format. The first and second columns must contain all connected scaffold pairs and the third column the number of connections.
`min_connections`	Filter all scaffold pairs with equal to or less than this number of connections. (Default: `2`)
`color_by`	Color the scaffolds by a variable in `mm`. (Default: `NULL`)
`color_scale_log10`	(Logical) Log10-scale the color gradient when `color_by` is set and the variable is continuous (Default: `FALSE`)
`locator`	(Logical) When `TRUE`, left-clicks in the plot are captured and the exact x/y-coordinates of the mouse clicks are captured and returned. These coordinates can be used to highlight a selection of scaffolds in the plot, and to extract all scaffolds within the selection. (Default: `FALSE`)
`selection`	A 2-column dataframe with the x and y coordinates of points with which to draw a polygon onto the plot to highlight a selected region. A selection can be obtained by using the locator feature (by `locator = TRUE`). (Default: `NULL`)
`highlight_labels`	A dataframe or vector of scaffold names whose labels to highlight in the plot (colored by `highlight_color`). (Default: `NULL`)
`highlight_color`	The color with which to highlight the scaffold labels defined by `highlight_labels`. (Default: `"darkred"`)
`links_scale`	A factor to scale the sizes of the links plotted between scaffolds. (Default: `1`)
`scaffold_labels`	Add labels with the scaffold names of all scaffolds.
`print_nolinks`	(Logical) Print the names of all scaffolds with no links to other scaffolds to the console. (Default: `FALSE`)
`seed`	Network plots are based on Random Number Generation, and this is used to set a specific random seed (with `set.seed`) allowing for reproducible network plots. Set to NULL to generate a unique network plot with each run of `mmnetwork`. (Default: `0`)

A ggplot object. Note that mmgenome2 hides all warnings produced by ggplot objects.

Unlike a plot generated by mmplot, the coordinates of points in each dimension in a mmnetwork plot is not contained within the provided dataframe mm itself. As such mmnetwork does not have a corresponding extract function like mmextract is for mmplot. Instead, a subset of mm containing all scaffolds within the selection polygon is available in the returned ggplot object with plot$data_in_selection.

Kasper Skytte Andersen ksa@bio.aau.dk

Soren M. Karst smk@bio.aau.dk

Mads Albertsen MadsAlbertsen85@gmail.com

library(mmgenome2)
data(mmgenome2)
data(paired_ends)
mmgenome2
selection <- data.frame(
  cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
  cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2, selection = selection)
mmgenome2_extraction
p <- mmnetwork(mmgenome2_extraction,
  network = paired_ends,
  min_connections = 1,
  color_by = "taxonomy"
)
p