plot_read_depth: View read depth
In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

plot_read_depth

R Documentation

View read depth

View read depth

plot_read_depth(physeq, xvar = NULL, lin = FALSE, cvar = NULL, clrs = NULL)

`physeq`	A phyloseq object
`xvar`	`NULL` A variable (column name) from `sample_data(physeq)` by which to group samples on the x-axis. Must be categorical. If `NULL`, no grouping will be performed.
`lin`	`FALSE` If `TRUE`, the y-axis will be on a linear scale. By default it is log-scaled.
`cvar`	`NULL` A variable (column name) from `sample_data(physeq)` by which the points should be coloured. If `NULL`, all points will be black. May be continuous or categorical. See the `clrs` argument if you want to specify your colours.
`clrs`	`NULL` If the `cvar` parameter is set and this is unset, colours will be taken from tax_colours if `cvar` is categorical and use ggplot2's default (blue) if `cvar` is continuous. If `cvar` is categorical, you may provide a named colour vector to use instead of tax_colours and if it is continuous you may provide a two-colour vector. The vector must have names "low" and "high". If `cvar` is NOT set, you may use this parameter to provide a single colour name or hex code that will be applied to all points.