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added option to load meta data #123

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merged 2 commits into from
Apr 11, 2024
Merged

added option to load meta data #123

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fc62e55
added option to load meta data
smuellerd Apr 11, 2024
d405bb6
removed code duplication
smuellerd Apr 11, 2024
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65 changes: 47 additions & 18 deletions R/utils-omnipath.R
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Original file line number Diff line number Diff line change
Expand Up @@ -85,12 +85,14 @@ get_dorothea <- function(organism='human', levels=c('A', 'B', 'C'),
#' @param organism Which organism to use. Only human, mouse and rat are available.
#' @param split_complexes Whether to split complexes into subunits. By default
#' complexes are kept as they are.
#' @param ... Ignored.
#' @param load_meta Whether to load meta data for the TF-gene interactions. This is set
#' to false by default.
#' @param ... Optional additional arguments, passed to OmniPath import_transcriptional_interactions.
#'
#' @export
#' @examples
#' collectri <- get_collectri(organism='human', split_complexes=FALSE)
get_collectri <- function(organism='human', split_complexes=FALSE, ...){
get_collectri <- function(organism='human', split_complexes=FALSE, load_meta=FALSE, ...){

# NSE vs. R CMD check workaround
source_genesymbol <- target_genesymbol <- weight <- NULL
Expand All @@ -104,6 +106,7 @@ get_collectri <- function(organism='human', split_complexes=FALSE, ...){
organism = organism,
genesymbol=TRUE,
loops=TRUE,
extra_attrs = TRUE,
...
),
error = function(e){
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This fallback won't have the extra_attrs column (though we can include it in the future). It raises a warning, so the user will be aware. Optionally we can handle the rare case when this happens with load_meta = TRUE.

Expand All @@ -122,9 +125,12 @@ get_collectri <- function(organism='human', split_complexes=FALSE, ...){
OmnipathR::import_tf_mirna_interactions(
genesymbols=TRUE,
resources = "CollecTRI",
strict_evidences = TRUE
strict_evidences = TRUE,
extra_attrs = TRUE
) %>%
base::rbind(collectri, .)
base::rbind(collectri, .) %>%
OmnipathR::extra_attrs_to_cols(sign_decision = CollecTRI_sign_decision,
TF_category = CollecTRI_tf_category)
},
error = function(e){
OmnipathR::omnipath_msg(
Expand All @@ -140,6 +146,10 @@ get_collectri <- function(organism='human', split_complexes=FALSE, ...){

cols <- c('source_genesymbol', 'target_genesymbol', 'is_stimulation',
'is_inhibition')

if (load_meta){
cols <- base::append(cols, c('sources', 'references', 'sign_decision', 'TF_category'))
}

collectri_interactions <- collectri[!stringr::str_detect(collectri$source,
"COMPLEX"), cols]
Expand All @@ -155,20 +165,39 @@ get_collectri <- function(organism='human', split_complexes=FALSE, ...){
stringr::str_detect(source_genesymbol, "NFKB") ~ "NFKB")
)
}

collectri <- base::rbind(collectri_interactions, collectri_complex) %>%
dplyr::distinct(source_genesymbol, target_genesymbol,
.keep_all = TRUE) %>%
dplyr::mutate(weight = dplyr::case_when(
is_stimulation == 1 ~ 1,
is_stimulation == 0 ~ -1
)) %>%
dplyr::select(source_genesymbol, target_genesymbol,
weight) %>%
dplyr::rename("source" = source_genesymbol,
"target" = target_genesymbol,
"mor" = weight,
)

if (!load_meta){
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This is a bit too much duplication, only little differences between the two branches

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Fixed :)

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Perfect, I think we can merge this :)

collectri <- base::rbind(collectri_interactions, collectri_complex) %>%
dplyr::distinct(source_genesymbol, target_genesymbol,
.keep_all = TRUE) %>%
dplyr::mutate(weight = dplyr::case_when(
is_stimulation == 1 ~ 1,
is_stimulation == 0 ~ -1
)) %>%
dplyr::select(source_genesymbol, target_genesymbol,
weight) %>%
dplyr::rename("source" = source_genesymbol,
"target" = target_genesymbol,
"mor" = weight)
} else {
collectri <- base::rbind(collectri_interactions, collectri_complex) %>%
dplyr::distinct(source_genesymbol, target_genesymbol,
.keep_all = TRUE) %>%
dplyr::mutate(weight = dplyr::case_when(
is_stimulation == 1 ~ 1,
is_stimulation == 0 ~ -1
)) %>%
dplyr::select(source_genesymbol, target_genesymbol,
weight, sources, references, sign_decision, TF_category) %>%
dplyr::mutate(references = stringr::str_extract_all(references, "\\d+")) %>%
dplyr::mutate(references = purrr::map_chr(references, ~paste(.x, collapse = ";"))) %>%
dplyr::rename("source" = source_genesymbol,
"target" = target_genesymbol,
"mor" = weight,
"resources" = sources,
"PMIDs" = references)
}

return(collectri)
}

Expand Down
2 changes: 2 additions & 0 deletions tests/testthat/test-omnipath.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,4 +35,6 @@ test_that("test get_collectri", {
testthat::expect_true(nrow(df) > 0)
df_split <- get_collectri(split_complexes=TRUE)
testthat::expect_true(nrow(df) < nrow(df_split))
df_split <- get_collectri(load_meta=TRUE)
testthat::expect_true(ncol(df) < ncol(df_split))
})
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