SQMtools (version 1.7.2)

exportPathway: 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,
  rescale_percent = FALSE,
  output_dir = ".",
  output_suffix = "pathview"
)

Value

A ggplot if split_samples = FALSE and the ggpattern package is installed, otherwise nothing. Additionally, Pathview figures will be written in the directory specified by output_dir.

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 median 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).

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).

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").

See Also

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

Examples

# \donttest{
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)
# }