mmplot: Visualise metagenomes in various ways
In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description Usage Arguments Value Author(s) Examples

Plots any information about the scaffolds contained in the given mm object as a scatterplot, for example different coverage variables, scaffold length, GC content, or anything else that were loaded with mmload. Scaffolds can then be highlighted and extracted using the locator and selection features.

mmplot(
  mm,
  x,
  y,
  min_length = 0,
  color_by = NULL,
  locator = FALSE,
  selection = NULL,
  network = NULL,
  shared_genes = FALSE,
  label_scaffolds = FALSE,
  label_scaffolds_by = "scaffold",
  label_bins = NULL,
  highlight_scaffolds = NULL,
  highlight_color = "darkred",
  x_scale = NULL,
  x_limits = NULL,
  y_scale = NULL,
  y_limits = NULL,
  alpha = 0.1,
  fixed_size = NULL,
  size_scale = 1,
  factor_shape = "outline",
  color_vector = c("blue", "green", "red"),
  color_scale_log10 = FALSE
)

`mm`	(required) A dataframe loaded with `mmload`.
`x`	(required) The variable from `mm` to plot on the first axis.
`y`	(required) The variable from `mm` to plot on the second axis.
`min_length`	Remove scaffolds with a length at or below this value before plotting. (Default: `0`)
`color_by`	Color the scaffolds by a variable in `mm`. (Default: `NULL`)
`locator`	(Logical) When `TRUE`, left-clicks in the plot are captured and the exact x/y-coordinates of the mouse clicks are returned. These coordinates can be used to highlight a selection of scaffolds in the plot, and also be used with `mmextract` to extract all scaffolds within the selection from the data. (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`)
`network`	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.
`shared_genes`	(Logical) If `TRUE`, lines will be drawn between scaffolds with any shared gene(s). (Default: `FALSE`)
`label_scaffolds`	Add text labels (with text from the variable in mm defined by `label_scaffolds_by`) to a selection of scaffolds by providing either a character vector of scaffold names, or a dataframe with scaffold names in the first column. If set to `TRUE` then all scaffolds will be labelled. (Default: `FALSE`)
`label_scaffolds_by`	The variable in mm by which to label the scaffolds defined by `label_scaffolds`. (Default: `"scaffold"`)
`label_bins`	Add labels at the centroids of bins (groups of scaffolds) defined by a variable in `mm`. (Default: `NULL`)
`highlight_scaffolds`	A vector of scaffold names or a dataframe loaded with `mmload` containing scaffolds to highlight in the plot with the color set by `highlight_color`. (Default: `NULL`)
`highlight_color`	The color with which to highlight the scaffolds set by `highlight`. (Default: `"darkred"`)
`x_scale`	Log10-scale (`"log10"`) or square-root scale `"sqrt"` the x axis. (Default: `NULL`)
`x_limits`	Axis limits of the x axis. Must be a vector of length 2 where the first number is the lower limit and the second number is the upper limit. Use `NA` to automatically detect the lowest and highest values, respectively. (Default: `NULL`)
`y_scale`	Log10-scale (`"log10"`) or square-root scale `"sqrt"` the y axis. (Default: `NULL`)
`y_limits`	Axis limits of the y axis. Must be a vector of length 2 where the first number is the lower limit and the second number is the upper limit. Use `NA` to automatically detect the lowest and highest values, respectively. (Default: `NULL`)
`alpha`	The transparancy of the scaffold points, where 0 is invisible and 1 is opaque. (Default: `0.1`)
`fixed_size`	A fixed size for all scaffolds if set. If `NULL` then the scaffolds are scaled by length. (Default: `NULL`)
`size_scale`	A factor to scale the sizes of the scaffolds plotted. Only applies when `fixed_size` is set to `NULL` and the scaffolds are scaled by length. (Default: `1`)
`factor_shape`	When `color_by` is a categorical variable (factor or character) then set the shape of the scaffolds to either `"solid"` or `"outline"`. (Default: `"outline"`)
`color_vector`	The colors from which to generate a color gradient when `color_by` is set and the variable is continuous. Any number of colors can be used. (Default: `c("blue", "green", "red")`)
`color_scale_log10`	(Logical) Log10-scale the color gradient when `color_by` is set and the variable is continuous. (Default: `FALSE`)

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

Kasper Skytte Andersen ksa@bio.aau.dk

Soren M. Karst smk@bio.aau.dk

Mads Albertsen MadsAlbertsen85@gmail.com

library(mmgenome2)
data(mmgenome2)
mmgenome2
mmplot(mmgenome2,
  min_length = 3000,
  x = "cov_C13.11.25",
  y = "cov_C14.01.09",
  color_by = "taxonomy",
  # locator = TRUE,
  x_scale = "log10",
  y_scale = "log10"
)
# Set "locator = TRUE" to interactively capture the coordinates of
# mouse clicks in an mmplot, or provide coordinates with "selection":
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)
)
mmplot(mmgenome2,
  min_length = 10000,
  x = "cov_C13.11.25",
  y = "cov_C14.01.09",
  color_by = "taxonomy",
  x_scale = "log10",
  y_scale = "log10",
  x_limits = c(1, NA), # zoom in at minimum 1x coverage
  y_limits = c(1, NA), # zoom in at minimum 1x coverage
  selection = selection
) # highlight the selection marked with locator