plotFunctions

plotFunctions

R Documentation

Heatmap of the most abundant functions in a SQM object

Description

This function selects the most abundant functions across all samples in a SQM object and represents their abundances in a heatmap. Alternatively, a custom set of functions can be represented.

Usage

plotFunctions(
  SQM,
  fun_level = "KEGG",
  count = "copy_number",
  N = 25,
  fun = NULL,
  samples = NULL,
  display_function_names = TRUE,
  ignore_unmapped = TRUE,
  ignore_unclassified = TRUE,
  gradient_col = c("ghostwhite", "dodgerblue4"),
  rescale_percent = FALSE,
  base_size = 11,
  metadata_groups = NULL
)

Arguments

`SQM`	A SQM, SQMbunch or SQMlite object.
`fun_level`	character. Either `"KEGG"`, `"COG"`, `"PFAM"` or any other custom database used for annotation (default `"KEGG"`).
`count`	character. Either `"abund"` for raw abundances, `"percent"` for percentages, `"bases"` for raw base counts, `"cpm"` for coverages per million reads, `"tpm"` for TPM normalized values or `"copy_number"` for copy numbers (default `"copy_number"`). Note that a given count type might not available in this object (e.g. TPM or copy number in SQMlite objects originating from a SQM reads project).
`N`	integer Plot the `N` most abundant functions (default `25`).
`fun`	character. Custom functions to plot. If provided, it will override `N` (default `NULL`).
`samples`	character. Character vector with the names of the samples to include in the plot. Can also be used to plot the samples in a custom order. If not provided, all samples will be plotted (default `NULL`).
`display_function_names`	logical. Plot function names alongside function IDs, if available (default `TRUE`).
`ignore_unmapped`	logical. Don’t include unmapped reads in the plot (default `TRUE`).
`ignore_unclassified`	logical. Don’t include unclassified ORFs in the plot (default `TRUE`).
`gradient_col`	A vector of two colors representing the low and high ends of the color gradient (default `c("ghostwhite", "dodgerblue4")`).
`rescale_percent`	logical. Calculate percent counts over the number of reads in the input object, instead of over the total number of reads in the original project (default `FALSE`).
`base_size`	numeric. Base font size (default `11`).
`metadata_groups`	list. Split the plot into groups defined by the user: list(‘G1’ = c(‘sample1’, sample2’), ‘G2’ = c(‘sample3’, ‘sample4’)) default `NULL`).

Value

a ggplot2 plot object.