lcms_plot_metabolites: Metabolite Candidates
In sipss/NIHSlcms: Signal processing of LC-MS metabolomics

Description Usage Arguments Value Examples

Post processing after obtaining the list of potential metabolite candidates. These metabolites can be filtered by biofluid and are sorted by p-value in ascending order. Unknown metabolites can be removed. After that, the results the results are plotted using a word cloud. The lower the p-value, the higher the font size of the metabolite. Additionally, we plot the a bar plot corresponding to the number of metabolites candidates associated to a single compound.

lcms_plot_metabolites(
  path_result,
  biofluid_type = "Any",
  significance = 0.05,
  metabolite_rm = TRUE,
  max_words = 250
)

`path_result`	The folder where the .csv file where the annotated table of metabolites is stored
`biofluid_type`	Filters the results by biofludid type.
`significance`	Filters the results by significance.
`metabolite_rm`	Logical. Remove "Unknown" metabolites.
`max_words`	Maximum number of words allowed in the word cloud.

Two plots: A word cloud with the potential identified metabolites and a bar plot with the number of potential cantidates by detected compound.

## Not run: 
path_result <-  system.file("extdata",
                            "results_project",
                            "tables",
                            "metaboliteTable.csv",
                            package = "AlpsLCMS")
plots <- lcms_plot_metabolites(path_result, biofluid_type = "Any",
                                   significance = 0.05,
                                   metabolite_rm = FALSE,
                                   max_words = 250)
plots$cloud

plots$freq

## End(Not run)