mmplot_pairs: Plot multiple combinations of variables in a pairs plot

In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description

Plots multiple variables from the given mm object in a grid plot with all pairs of variables using mmplot.

Usage

mmplot_pairs(mm, variables = NULL, textsize = 5, axis_ticks = TRUE, ...)

Arguments

mm	(required) A dataframe loaded with mmload.
variables	A vector of 3 or more variable names in mm to plot on each axis. If NULL, the default, then all coverage variables will be plotted as well as GC content. (Default: NULL)
textsize	The text size of the axis titles. (Default: 5)
axis_ticks	Hide or show axis ticks on both axes. (Default: TRUE)
...	Arguments passed on to mmplot, eg. color_by, min_length, axis scales and more, see help("mmplot").

Value

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

Author(s)

Kasper Skytte Andersen [e-mail]

Soren M. Karst [e-mail]

Mads Albertsen [e-mail]

Examples

library(mmgenome2)
data(mmgenome2)
mmgenome2
mmplot_pairs(mmgenome2,
  variables = c("cov_C13.11.14", "cov_C13.11.25", "cov_C13.12.03", "cov_C14.01.09"),
  min_length = 10000,
  color_by = "taxonomy",
  x_scale = "log10",
  y_scale = "log10",
  x_limits = c(1, NA),
  y_limits = c(1, NA)
)

KasperSkytte/mmgenome2 documentation built on Dec. 14, 2021, 12:11 a.m.