plotFunctions {SQMtools}

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 = "tpm",
  N = 25,
  fun = NULL,
  samples = NULL,
  ignore_unmapped = TRUE,
  ignore_unclassified = TRUE,
  gradient_col = c("ghostwhite", "dodgerblue4"),
  base_size = 11,
  metadata_groups = NULL
)

Arguments

SQM

A SQM 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 "tpm"). 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).

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")).

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.

See Also

plotTaxonomy for plotting the most abundant taxa of a SQM object; plotBars and plotHeatmap for plotting barplots or heatmaps with arbitrary data.

Examples

data(Hadza)
plotFunctions(Hadza)