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fixed passing source organism in get_homologene_dict: fixes #170 #174

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fixed passing source organism in get_homologene_dict: fixes #170 #174

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d1051c0
updated `Remotes` of `basilisk`: `LTLA` → `Bioconductor`
deeenes Aug 22, 2024
f535344
`get_homologene_dict`: no NSE on organisms (fails if integer is provi…
deeenes Aug 29, 2024
4b807e3
`.handle_complexes`: do not fail on empty vector
deeenes Aug 29, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,6 @@ Suggests:
muscData,
broom
biocViews: scater, scran, SingleCellExperiment, ComplexHeatmap, muscData, ExperimentHub
Remotes: sqjin/CellChat, saezlab/OmnipathR, saezlab/decoupleR, LTLA/basilisk.utils, LTLA/basilisk
RoxygenNote: 7.2.3
Remotes: sqjin/CellChat, saezlab/OmnipathR, saezlab/decoupleR, Bioconductor/basilisk.utils, Bioconductor/basilisk
RoxygenNote: 7.3.0
Config/testthat/edition: 3
11 changes: 9 additions & 2 deletions R/liana_ortho.R
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Expand Up @@ -58,7 +58,6 @@ generate_homologs <- function(op_resource,
symbols_dict <- get_homologene_dict(entities = entities,
target_organism = target_organism)


# Remove any missing antities
if(is.null(.missing_fun)){

Expand Down Expand Up @@ -254,7 +253,15 @@ recode.character2 <- function(.x,
.default = NULL,
.missing = NULL,
.missing_fun) {

.x <- as.character(.x)

if (length(.x) == 0) {

return(.x)

}

values <- rlang::list2(...)
if (!all(rlang::have_name(values))) {
bad <- which(!rlang::have_name(values)) + 1
Expand Down Expand Up @@ -399,7 +406,7 @@ get_homologene_dict <- function(entities,
id_type = "genesymbol"){

# Load homology geneset
hg_gs <- homologene_download(target = !!target_organism,
hg_gs <- homologene_download(target = target_organism,
source = 9606L, # always human
id_type = !!id_type) %>%
select(-hgroup) %>%
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