From 7a3c0de232a20320d4e83b28db6ab4524857424f Mon Sep 17 00:00:00 2001 From: deeenes Date: Mon, 22 May 2023 18:47:55 +0200 Subject: [PATCH] pkgdown site rebuild --- R/evidences.R | 5 +- docs/LICENSE-text.html | 2 +- docs/authors.html | 2 +- docs/reference/collectri.html | 31 ++- docs/reference/dorothea.html | 15 +- docs/reference/ensure_igraph.html | 2 +- docs/reference/filter_evidences.html | 144 ++++++++++++++ docs/reference/from_evidences.html | 176 ++++++++++++++++++ docs/reference/graph_interaction.html | 2 +- docs/reference/import_all_interactions.html | 9 +- .../import_kinaseextra_interactions.html | 9 +- .../import_ligrecextra_interactions.html | 9 +- .../import_lncrna_mrna_interactions.html | 9 +- .../import_mirnatarget_interactions.html | 9 +- .../import_omnipath_interactions.html | 9 +- .../import_pathwayextra_interactions.html | 9 +- ...mport_post_translational_interactions.html | 9 +- ...t_small_molecule_protein_interactions.html | 25 +-- .../import_tf_mirna_interactions.html | 9 +- .../import_tf_target_interactions.html | 9 +- .../import_transcriptional_interactions.html | 9 +- docs/reference/index.html | 22 ++- docs/reference/interaction_graph.html | 4 +- docs/reference/omnipath.html | 19 +- docs/reference/only_from.html | 164 ++++++++++++++++ docs/reference/unnest_evidences.html | 147 +++++++++++++++ 26 files changed, 799 insertions(+), 60 deletions(-) create mode 100644 docs/reference/filter_evidences.html create mode 100644 docs/reference/from_evidences.html create mode 100644 docs/reference/only_from.html create mode 100644 docs/reference/unnest_evidences.html diff --git a/R/evidences.R b/R/evidences.R index dc8a17a0..48581602 100644 --- a/R/evidences.R +++ b/R/evidences.R @@ -339,10 +339,11 @@ only_from <- function(data, datasets = NULL, resources = NULL) { #' #' @examples #' ci <- collectri(evidences = TRUE) +#' ci <- unnest_evidences(ci) #' ci <- filter_evidences(datasets = 'collectri') #' ci <- from_evidences(ci) -#' # the two lines above are equivalent to only_from(ci) -#' # and all the three lines above is equivalent to: +#' # the three lines above are equivalent to only_from(ci) +#' # and all the four lines above is equivalent to: #' # collectri(strict_evidences = TRUE) #' #' @importFrom magrittr %>% diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index cbff7d6a..e3e649bc 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -16,7 +16,7 @@ OmnipathR - 3.9.2 + 3.9.3 + + + + + +
+
+
+

Filter evidences by dataset and resource

+ Source: R/evidences.R +
filter_evidences.Rd
+
+ +
+

Filter evidences by dataset and resource

+
+ +
+

Usage

+ 
filter_evidences(data, ..., datasets = NULL, resources = NULL)
+
+ +
+

Arguments

+
data
+

An interaction data frame with some columns containing evidences +as nested lists.

+ + +
...
+

The evidences columns to filter: tidyselect syntax is supported. +By default the columns "evidences", "positive", "negative", "directed" +and "undirected" are filtered, if present.

+ + +
datasets
+

A character vector of dataset names.

+ + +
resources
+

A character vector of resource names.

+ +
+
+

Value

+ + +

The input data frame with the evidences in the selected columns + filtered.

+
+
+

See also

+
+
+
+ +
+ + +
+

Developed by Alberto Valdeolivas, Denes Turei, Attila Gabor.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/from_evidences.html b/docs/reference/from_evidences.html new file mode 100644 index 00000000..4fadbb07 --- /dev/null +++ b/docs/reference/from_evidences.html @@ -0,0 +1,176 @@ + +Recreate interaction records from evidences columns — from_evidences • OmnipathR + Skip to contents + + +
+
+
+

Recreate interaction records from evidences columns

+ Source: R/evidences.R +
from_evidences.Rd
+
+ +
+

Recreate interaction records from evidences columns

+
+ +
+

Usage

+ 
from_evidences(data)
+
+ +
+

Arguments

+
data
+

An interaction data frame from the OmniPath web service with +evidences column.

+ +
+
+

Value

+ + +

A copy of the input data frame with all the standard columns + describing the direction, effect, resources and references of the + interactions recreated based on the contents of the nested list + evidences column(s).

+
+
+

Details

+

The OmniPath interaction data frames specify interactions primarily by +three columns: "is_directed", "is_stimulation" and "is_inhibition". +Besides these, there are the "sources" and "references" columns that are +always included in data frames created by OmnipathR and list the resources +and literature references for each interaction, respectively. The optional +"evidences" column is required to find out which of the resources and +references support the direction or effect sign of the interaction. To +properly recover information for arbitrary subsets of resources or +datasets, the evidences can be filtered first, and then the standard +data frame columns can be reconstructed from the selected evidences. +This function is able to do the latter. It expects either an "evidences" +column or evidences in their wide format 4 columns layout. It overwrites +the standard columns of interaction records based on data extracted from +the evidences, including the "curation_effort" and "consensus..." columns.

+

Note: The "curation_effort" might be calculated slightly +differently from the version included in the OmniPath web service. Here +we count the resources and the also add the number of references for each +resource. E.g. a resource without any literatur reference counts as 1, +while a resource with 3 references adds 4 to the value of the curation +effort.

+

Note: If the "evidences" column has been already unnested to +multiple columns ("positive", "negative", etc.) by +unnest_evidences, then these will be used; +otherwise, the column will be unnested within this function.

+

Note: This function (or rather its wrapper, +only_from) is automatically applied if the `strict_evidences` +argument is passed to any function querying interactions (e.g. +import_omnipath_interactions).

+
+
+

See also

+
+
+
+ +
+

Examples

+ 
ci <- collectri(evidences = TRUE)
+ci <- filter_evidences(datasets = 'collectri')
+#> Error: argument "data" is missing, with no default
+ci <- from_evidences(ci)
+#> Error in do.call(stop, list(m), envir = env): `from_evidences` can be called only on data frames with `evidences` column.
+# the two lines above are equivalent to only_from(ci)
+# and all the three lines above is equivalent to:
+# collectri(strict_evidences = TRUE)
+
+
+
+
+ + +
+

Developed by Alberto Valdeolivas, Denes Turei, Attila Gabor.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/graph_interaction.html b/docs/reference/graph_interaction.html index 04100f97..46c6812d 100644 --- a/docs/reference/graph_interaction.html +++ b/docs/reference/graph_interaction.html @@ -24,7 +24,7 @@ OmnipathR - 3.9.1 + 3.9.3 + + + + + +
+
+
+

Recreate interaction data frame based on certain datasets and resources

+ Source: R/evidences.R +
only_from.Rd
+
+ +
+

Recreate interaction data frame based on certain datasets and resources

+
+ +
+

Usage

+ 
only_from(data, datasets = NULL, resources = NULL)
+
+ +
+

Arguments

+
data
+

An interaction data frame from the OmniPath web service with +evidences column.

+ + +
datasets
+

Character: a vector of dataset labels. Only evidences from +these datasets will be used.

+ + +
resources
+

Character: a vector of resource labels. Only evidences +from these resources will be used.

+ +
+
+

Value

+ + +

A copy of the interaction data frame restricted to the given + datasets and resources.

+
+
+

Details

+

The OmniPath interactions database fully integrates all attributes from all +resources for each interaction. This comes with the advantage that +interaction data frames are ready for use in most of the applications; +however, it makes it impossible to know which of the resources and +references support the direction or effect sign of the interaction. This +information can be recovered from the "evidences" column. The "evidences" +column preserves all the details about interaction provenances. In cases +when you want to use a faithful copy of a certain resource or dataset, this +function will help you do so. Still, in most of the applications the best is +to use the interaction data as it is returned by the web service.

+

Note: This function is automatically applied if the +`strict_evidences` argument is passed to any function querying interactions +(e.g. import_omnipath_interactions).

+
+
+

See also

+
+
+
+ +
+

Examples

+ 
ci <- collectri(evidences = TRUE)
+ci <- only_from(ci, datasets = 'collectri')
+#> Error in do.call(stop, list(m), envir = env): `only_from` can be called only on data frames with `evidences` column.
+
+
+
+
+ + +
+

Developed by Alberto Valdeolivas, Denes Turei, Attila Gabor.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/unnest_evidences.html b/docs/reference/unnest_evidences.html new file mode 100644 index 00000000..4d071445 --- /dev/null +++ b/docs/reference/unnest_evidences.html @@ -0,0 +1,147 @@ + +Separate evidences by direction and effect sign — unnest_evidences • OmnipathR + Skip to contents + + +
+
+
+

Separate evidences by direction and effect sign

+ Source: R/evidences.R +
unnest_evidences.Rd
+
+ +
+

Separate evidences by direction and effect sign

+
+ +
+

Usage

+ 
unnest_evidences(data, longer = FALSE)
+
+ +
+

Arguments

+
data
+

An interaction data frame with "evidences" column.

+ + +
longer
+

Logical: If TRUE, the "evidences" column is split into rows.

+ +
+
+

Value

+ + +

The data frame with new columns or new rows by direction and sign.

+
+
+

See also

+
+
+
+ +
+

Examples

+ 
omnipath <- import_omnipath_interactions(fields = 'evidences')
+omnipath <- unnest_evidences(omnipath)
+colnames(omnipath)
+#>  [1] "source"                "target"                "source_genesymbol"    
+#>  [4] "target_genesymbol"     "is_directed"           "is_stimulation"       
+#>  [7] "is_inhibition"         "consensus_direction"   "consensus_stimulation"
+#> [10] "consensus_inhibition"  "positive"              "negative"             
+#> [13] "directed"              "undirected"            "sources"              
+#> [16] "references"            "curation_effort"       "n_references"         
+#> [19] "n_resources"          
+
+
+
+
+ + +
+ + + + + + +