package-deprecated: deprecated functions - to be removed in RaMP 4.0
In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

pathwayResultsPlot

R Documentation

deprecated functions - to be removed in RaMP 4.0

Description

Use plotPathwayResults instead of pathwayResultsPlot

Use getChemClass instead of chemicalClassSurvey

Use runEnrichChemClass instead of chemicalClassEnrichment

Use filterEnrichResults instead of FilterFishersResults

Use writeFishersResults instead of write_FishersResults

Use runEnrichPathways instead of runCombinedFisherTest

Usage

pathwayResultsPlot(
  db = RaMP(),
  pathwaysSig,
  pval = "FDR",
  perc_analyte_overlap = 0.5,
  perc_pathway_overlap = 0.5,
  min_pathway_tocluster = 3,
  text_size = 8,
  sig_cutoff = 0.05,
  interactive = FALSE
)

chemicalClassSurvey(
  db = RaMP(),
  mets,
  background = "database",
  background_type = "database",
  includeRaMPids = FALSE,
  inferIdMapping = TRUE
)

chemicalClassEnrichment(
  db = RaMP(),
  mets,
  background = "database",
  background_type = "database",
  inferIdMapping = F
)

FilterFishersResults(fishers_df, pval_type = "fdr", pval_cutoff = 0.1)

write_FishersResults(fishResults = "none", outputfile = "none", rampid = FALSE)

runCombinedFisherTest(
  db = RaMP(),
  analytes,
  NameOrIds = "ids",
  total_genes = 20000,
  min_analyte = 2,
  MCall = F,
  alternative = "less",
  min_path_size = 5,
  max_path_size = 150,
  includeRaMPids = FALSE,
  background_type = "database",
  background = "database",
  pathway_definitions = "RaMP",
  include_smpdb = FALSE
)

Arguments

`db`	a RaMP databse object
`pathwaysSig`	output of FilterFisherResults
`pval`	Which p value to plot, choose from Raw, FDR or Holm-adjusted
`perc_analyte_overlap`	Minimum overlap for pathways to be considered similar (Default = 0.2)
`perc_pathway_overlap`	Minimum overlap for clusters to merge (Default = 0.2)
`min_pathway_tocluster`	Minimum number of 'similar' pathways required to start a cluster (medoid) (Default = 3)
`text_size`	Scales all text in figure (Default=16)
`sig_cutoff`	Aesthetic, shows pvalue cutoff for significant pathways
`interactive`	If TRUE, return interactive plotly object instead of ggplot object
`mets`	a vector of source prepended metabolite ids
`background`	background to be used for Fisher's tests. If parameter 'background_type="database"', this parameter is ignored (default="database"); if parameter 'background_type= "file"', then 'background' should be a file name (with directory); if 'background_type="list"', then 'background' should be a vector of RaMP IDs; if 'backgroud_type="biospecimen"' then users should specify one of the following: "Blood", "Adipose tissue", "Heart", "Urine", "Brain", "Liver", "Kidney", "Saliva", and "Feces"
`background_type`	type of background that is input by the user. Opions are "database" if user wants all analytes from the RaMP database to be used as background; "file", if user wnats to input a file path with a list of background analytes; "list", if user wants to input a vector of analyte IDs; "biospecimen", if user wants to specify a biospecimen type (e.g. blood, adipose tissue, etc.) and have those biospecimen-specific analytes used. For genes, only the "database" option is used.
`includeRaMPids`	include internal RaMP identifiers (default is "FALSE")
`inferIdMapping`	if FALSE, the method only reports on class annotations made directly on the input ids. If inferIdMapping is set to TRUE, the input ids are cross-referenced or mapped to other existing ids that contain metabolite class annotations. Following id cross references can expand coverage if the input type is other than HMDB ids or LIPIDMAPS ids. The default value is FALSE.
`fishers_df`	The data frame generated by runFisherTest
`pval_type`	Specifies which p-value to use as the filter threshold. Permitted values are 'pval' and 'fdr' for chemical class and pathway enrichment. Pathway enrichment also includes an optional 'holm' value for holm p-value corrections. Default is 'fdr'.
`pval_cutoff`	return pathways where pval_type p-values are < pval_cutoff
`fishResults`	a data frame returned by function runCombinedFisherTest()
`outputfile`	name of output file
`rampid`	whether or not to include rampId (default is FALSE)
`analytes`	a vector of analytes (genes or metabolites) that need to be searched
`NameOrIds`	whether input is "names" or "ids" (default is "ids", must be the same for analytes and background)
`total_genes`	number of genes analyzed in the experiment (e.g. background) (default is 20000, with assumption that analyte_type is "genes")
`min_analyte`	if the number of analytes (gene or metabolite) in a pathway is < min_analyte, do not report
`MCall`	T/F if true, all pathways are used for multiple comparison corrections; if false, only pathways covering user analytes will be used (default is "F")
`alternative`	alternative hypothesis test passed on to fisher.test(). Options are two.sided, greater, or less (default is "less")
`min_path_size`	the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5)
`max_path_size`	the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150)
`pathway_definitions`	If "RaMP" (default), use pathway definitions within RaMP-DB. Else, supply path to gmx file containing custom pathway definitions. GMX files are a tab-separated format that contain one analyte set per column, with the name of the set in the first row, and constituent analytes in subsequent rows. Please supply a .xls or .xlsx file. If supplying pathway definitions for genes and metabolites, ensure that metabolite definitions are on tab 1, and gene definitions are on tab2.
`include_smpdb`	Include pathways from smpdb/hmdb in analysis. Excluded by default since definitions are highly redundant