exportPathway: Export the functions of a SQM object into KEGG pathway maps

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

Export the functions of a SQM object into KEGG pathway maps

Description

This function is a wrapper for the pathview package (Luo et al., 2017. Nucleic acids research, 45:W501-W508). It will generate annotated KEGG pathway maps showing which reactions are present in the different samples. It will also generate legends with the color scales for each sample in separate png files.

Usage

exportPathway(
  SQM,
  pathway_id,
  count = "copy_number",
  samples = NULL,
  split_samples = FALSE,
  sample_colors = NULL,
  log_scale = FALSE,
  fold_change_groups = NULL,
  fold_change_colors = NULL,
  max_scale_value = NULL,
  color_bins = 10,
  output_dir = ".",
  output_suffix = "pathview"
)

Arguments

SQM	A SQM, SQMbunch or SQMlite object.
pathway_id	character. The five-number KEGG pathway identifier. A list of all pathway identifiers can be found in https://www.genome.jp/kegg/pathway.html.
count	character. Either "abund" for raw abundances, "percent" for percentages, "bases" for raw base counts, "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).
samples	character. An optional vector with the names of the samples to export. If absent, all samples will be exported (default NULL).
split_samples	logical. Generate a different output file for each sample (default FALSE).
sample_colors	character. An optional vector with the plotting colors for each sample (default NULL).
log_scale	logical. Use a base 10 logarithmic transformation for the color scale. Will have no effect if fold_change_groups is provided (default FALSE).
fold_change_groups	list. An optional list containing two vectors of samples. If provided, the function will generate a single plot displaying the log2 fold-change between the average abundances of both groups of samples ( log(second group / first group) ) (default NULL).
fold_change_colors	character. An optional vector with the plotting colors of both groups in the fold-change plot. Will be ignored if fold_change_group is not provided.
max_scale_value	numeric. Maximum value to include in the color scale. By default it is the maximum value in the selected samples (if plotting abundances in samples) or the maximum absolute log2 fold-change (if plotting fold changes) (default NULL).
color_bins	numeric. Number of bins used to generate the gradient in the color scale (default 10).
output_dir	character. Directory in which to write the output files (default ".").
output_suffix	character. Suffix to be added to the output files (default "pathview").

Value

No return value, but Pathview figures are produced in the current working directory.

See Also

plotFunctions for plotting the most functions taxa of a SQM object.

Examples

data(Hadza)

exportPathway(Hadza, "00910", count = 'copy_number',
              output_dir = tempdir(),
              output_suffix = "nitrogen_metabolism",
              sample_colors = c("red", "blue"))
exportPathway(Hadza, "00250", count = 'tpm',
              output_dir = tempdir(),
              output_suffix = "ala_asp_glu_metabolism_FoldChange", 
              fold_change_groups = list(c("H1"), c("H12")), max_scale_value=2)

SQMtools documentation built on April 3, 2025, 6:16 p.m.