| validateCreateEnrichMapMultiComplexArg | R Documentation |
Validate arguments passed to validateCreateEnrichMapMultiComplex()
function
Description
Validate the arguments passed to
validateCreateEnrichMapMultiComplex() function.
First, the object containing the enrichment results must correspond to a
object created by gprofiler2 software. Second, the selected
source must at least have one enriched term in the results. Then, if the
source is 'TERM_ID', the listed terms must be present in the enrichment
results.
Usage
validateCreateEnrichMapMultiComplexArg(
gostObjectList,
queryInfo,
showCategory,
groupCategory,
categoryLabel,
categoryNode,
line
)
Arguments
gostObjectList |
a list of gprofiler2 objects that
contain the results from an enrichment analysis. The list must contain at
least 2 entries. The number of entries must correspond to the number of
entries for the queryList parameter.
|
queryInfo |
a data.frame contains one row per group being
displayed. The number of rows must correspond to the
number of entries for the gostObjectList parameter.
The mandatory columns are:
queryName: a character string representing the name
of the query retained for this group). The query names must exist in the
associated gostObjectList objects and follow the same order.
source: a character string representing the selected
source that will be used to generate the network. To hand-pick the terms to
be used, "TERM_ID" should be used and the list of selected term IDs should
be passed through the termIDs parameter. The possible sources are
"GO:BP" for Gene Ontology Biological Process, "GO:CC" for Gene Ontology
Cellular Component, "GO:MF" for Gene Ontology Molecular Function,
"KEGG" for Kegg, "REAC" for Reactome, "TF" for TRANSFAC, "MIRNA" for
miRTarBase, "CORUM" for CORUM database, "HP" for Human phenotype ontology
and "WP" for WikiPathways. Default: "TERM_ID".
removeRoot: a logical that specified if the root terms
of the selected source should be removed (when present).
termIDs: a character strings that contains the
term IDS retained for the creation of the network separated by a comma ','
when the "TERM_ID" source is selected. Otherwise, it should be a empty
string ("").
groupName: a character strings that contains the
name of the group to be shown in the legend. Each group has to have a
unique name.
|
showCategory |
a positive integer or a vector of
characters representing terms. If a integer, the first
n terms will be displayed. If vector of terms,
the selected terms will be displayed.
|
groupCategory |
a logical indicating if the categories should
be grouped.
|
categoryLabel |
a positive numeric representing the amount by
which plotting category nodes label size should be scaled relative
to the default (1).
|
categoryNode |
a positive numeric representing he amount by
which plotting category nodes should be scaled relative to the default (1).
|
line |
a non-negative numeric representing the scale of line
width.
|
Value
TRUE when all arguments are valid
Author(s)
Astrid Deschênes
Examples
## Load the result of an enrichment analysis done with gprofiler2
data(parentalNapaVsDMSOEnrichment)
data(rosaNapaVsDMSOEnrichment)
queryDataFrame <- data.frame(queryName=c("parental_napa_vs_DMSO",
"rosa_napa_vs_DMSO"), source=c("KEGG", "WP"), removeRoot=c(TRUE, TRUE),
termIDs=c("", ""), groupName=c("parental - KEGG", "rosa - WP"),
stringsAsFactors=FALSE)
## Check that all arguments are valid
enrichViewNet:::validateCreateEnrichMapMultiComplexArg(
gostObjectList=list(parentalNapaVsDMSOEnrichment,
rosaNapaVsDMSOEnrichment),
queryInfo=queryDataFrame,
showCategory=20, groupCategory=FALSE,
categoryLabel=1.1, categoryNode=1, line=1.2)
