genomic_func_heatmap: Genomic Functional Heatmap

Description Usage Arguments

View source: R/plot-genome-function.R

Description

This function will crteate a heatmap, either static (via ggplot2) or interactive (via plotly), that will allow for the visualization of genomes in a given dataset that complete different functions

Usage

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genomic_func_heatmap(data, otu_tibble = NULL, tax_tibble = NULL,
  ps_orig = NULL, interactive = TRUE, relative_abundance = FALSE,
  abundance_threshold = NULL, relative_abundance_threshold = NULL)

Arguments

data

The output from either the has_complete_function or has_specific_function. If the output of has_complete_function is used, then it should be filtered to include only the desired modules prior to being passed into this function.

otu_tibble,

tax_tibble the output from otu_tibble and tax_tibble, respectively. Both of of these must be given or 'ps_orig' must be specified

ps_orig

the original phyloseq object that was used to create dataset passed to the 'data' argument

interactive

default TRUE; if TRUE, then the heatmap will be plotted with plotly. If FALSE, then the heatmap will be generated with ggplot2

relative_abundance

default FALSE; if TRUE the heatmap will use relative abundance as its fill color. If FALSE then abundance will be used

abundance_threshold

default NULL; The minimum abundance number required to be included in the heatmap

relative_abundance_threshold

default NULL; The minimum percent relative abundance requied to be included in the heatmap


tbradley1013/KEGGerator documentation built on Feb. 23, 2020, 6:44 a.m.