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Add BioGRID column in link table
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@csoneson
csoneson committed May 2, 2024
1 parent 6c925cf commit 26cd706
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1 change: 1 addition & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
* Expand input data paths in run*Analysis() functions
* Add support for importing Spectronaut PG pivot files
* Add initial support for reading Spectronaut setup.txt files
* Add BioGRID column in link table

# einprot 0.9.3

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19 changes: 14 additions & 5 deletions R/makeDbLinkTable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ formatTableColumns <- function(tbl, columns, signifDigits, maxLevels = 10) {
.assertScalar(x = id, type = "character")
.assertScalar(x = linktype, type = "character",
validValues = c("UniProt", "AlphaFold", "PomBase",
"WormBase", "ComplexPortal"))
"WormBase", "ComplexPortal", "BioGRID"))

if (!is.na(id) && id != "") {
if (removeSuffix) {
Expand All @@ -91,6 +91,9 @@ formatTableColumns <- function(tbl, columns, signifDigits, maxLevels = 10) {
} else if (linktype == "ComplexPortal") {
sprintf('<a href="%s" target="_blank"> %s</a>',
paste0("https://www.ebi.ac.uk/complexportal/complex/search?query=", id), id)
} else if (linktype == "BioGRID") {
sprintf('<a href="%s" target="_blank"> %s</a>',
paste0("https://thebiogrid.org/search.php?search=", id, "&organism=all"), id)
} else {
""
}
Expand Down Expand Up @@ -179,8 +182,8 @@ getConvTable <- function(type) {
#' generated using \code{getConvTable(type = "WormBase")}.
#' @param removeSuffix Logical scalar indicating whether suffixes of the
#' form \code{-[0-9]+} should be removed from the protein ID before
#' generating the URL. Currently only influencing the AlphaFold and
#' ComplexPortal URLs.
#' generating the URL. Currently only influencing the AlphaFold,
#' ComplexPortal and BioGRID URLs.
#' @param signifDigits Numeric scalar giving the number of significant digits
#' to round numeric columns to. If \code{NULL}, no rounding will be
#' performed.
Expand Down Expand Up @@ -226,7 +229,7 @@ makeDbLinkTable <- function(df, idCol, speciesCommon,
.assertScalar(x = signifDigits, type = "numeric", allowNULL = TRUE)

## -------------------------------------------------------------------------
## Create UniProt and AlphaFold columns
## Create UniProt, AlphaFold, ComplexPortal and BioGRID columns
## -------------------------------------------------------------------------
linkTable <- df %>%
dplyr::mutate(UniProt = vapply(.data[[idCol]], function(mpds) {
Expand All @@ -246,6 +249,12 @@ makeDbLinkTable <- function(df, idCol, speciesCommon,
.makeLinkFromId(mpd, linktype = "ComplexPortal",
removeSuffix = removeSuffix)
}, ""), collapse = ";")
}, "NA")) %>%
dplyr::mutate(BioGRID = vapply(.data[[idCol]], function(mpds) {
paste(vapply(strsplit(mpds, ";")[[1]], function(mpd) {
.makeLinkFromId(mpd, linktype = "BioGRID",
removeSuffix = removeSuffix)
}, ""), collapse = ";")
}, "NA"))

if (addSpeciesSpecificColumns &&
Expand Down Expand Up @@ -309,7 +318,7 @@ makeDbLinkTable <- function(df, idCol, speciesCommon,
linkTable <- formatTableColumns(
tbl = linkTable,
columns = setdiff(colnames(linkTable), c("UniProt", "AlphaFold",
"ComplexPortal",
"ComplexPortal", "BioGRID",
"WormBase", "PomBase")),
signifDigits = signifDigits, maxLevels = 10)

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4 changes: 2 additions & 2 deletions man/makeDbLinkTable.Rd
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72 changes: 56 additions & 16 deletions tests/testthat/test-makeDbLinkTable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,10 @@ test_that("making the link table works", {
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=Q7YTG1" target="_blank"> Q7YTG1</a>')
expect_equal(.makeLinkFromId("Q7YTG1-1", "ComplexPortal", removeSuffix = FALSE),
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=Q7YTG1-1" target="_blank"> Q7YTG1-1</a>')
expect_equal(.makeLinkFromId("Q7YTG1-1", "BioGRID", removeSuffix = TRUE),
'<a href="https://thebiogrid.org/search.php?search=Q7YTG1&organism=all" target="_blank"> Q7YTG1</a>')
expect_equal(.makeLinkFromId("Q7YTG1-1", "BioGRID", removeSuffix = FALSE),
'<a href="https://thebiogrid.org/search.php?search=Q7YTG1-1&organism=all" target="_blank"> Q7YTG1-1</a>')

## getConvTable
## -------------------------------------------------------------------------
Expand Down Expand Up @@ -186,10 +190,10 @@ test_that("making the link table works", {
idCol = "id", speciesCommon = "fission yeast",
signifDigits = 3)
expect_s3_class(dblt, "data.frame")
expect_equal(ncol(dblt), 6)
expect_equal(ncol(dblt), 7)
expect_equal(nrow(dblt), 3)
expect_named(dblt, c("id", "numcol", "intcol", "UniProt", "AlphaFold",
"ComplexPortal"))
"ComplexPortal", "BioGRID"))
expect_equal(dblt$id, factor(c("B5BP45", "O13282", "B5BP45")))
expect_equal(dblt$numcol, c(1.23, 0.000346, 7630))
expect_type(dblt$intcol, "integer")
Expand All @@ -209,16 +213,22 @@ test_that("making the link table works", {
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>',
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=B5BP45" target="_blank"> B5BP45</a>'),
ignore_attr = TRUE)
expect_equal(dblt$BioGRID, c(
'<a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>',
'<a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>',
'<a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>'),
ignore_attr = TRUE)

## As above, but different number of significant digits
dblt <- makeDbLinkTable(data.frame(id = c("B5BP45", "O13282", "O13282"),
numcol = c(1.23456, 0.00034561, 7625.23)),
idCol = "id", speciesCommon = "fission yeast",
signifDigits = 1)
expect_s3_class(dblt, "data.frame")
expect_equal(ncol(dblt), 5)
expect_equal(ncol(dblt), 6)
expect_equal(nrow(dblt), 3)
expect_named(dblt, c("id", "numcol", "UniProt", "AlphaFold", "ComplexPortal"))
expect_named(dblt, c("id", "numcol", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID"))
expect_equal(dblt$id, factor(c("B5BP45", "O13282", "O13282")))
expect_equal(dblt$numcol, c(1, 0.0003, 8000))
expect_equal(dblt$UniProt, c(
Expand All @@ -236,6 +246,11 @@ test_that("making the link table works", {
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>',
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>'),
ignore_attr = TRUE)
expect_equal(dblt$BioGRID, c(
'<a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>',
'<a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>',
'<a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>'),
ignore_attr = TRUE)

## With Pombase column
dblt2 <- makeDbLinkTable(
Expand All @@ -245,9 +260,10 @@ test_that("making the link table works", {
PomBaseID = c("SPCC5E4.03c", "SPBC460.01c"),
UniProtID = c("O13282", "B5BP45")))
expect_s3_class(dblt2, "data.frame")
expect_equal(ncol(dblt2), 5)
expect_equal(ncol(dblt2), 6)
expect_equal(nrow(dblt2), 2)
expect_named(dblt2, c("id", "UniProt", "AlphaFold", "ComplexPortal", "PomBase"))
expect_named(dblt2, c("id", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID", "PomBase"))
expect_equal(dblt2$id, factor(c("B5BP45", "O13282")))
expect_equal(dblt2$UniProt, c(
'<a href="https://www.uniprot.org/uniprot/B5BP45" target="_blank"> B5BP45</a>',
Expand All @@ -261,6 +277,10 @@ test_that("making the link table works", {
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=B5BP45" target="_blank"> B5BP45</a>',
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>'),
ignore_attr = TRUE)
expect_equal(dblt2$BioGRID, c(
'<a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>',
'<a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>'),
ignore_attr = TRUE)
expect_equal(dblt2$PomBase, c(
'<a href=\"https://www.pombase.org/gene/SPBC460.01c\" target=\"_blank\"> SPBC460.01c</a>',
'<a href=\"https://www.pombase.org/gene/SPCC5E4.03c\" target=\"_blank\"> SPCC5E4.03c</a>'),
Expand All @@ -274,9 +294,10 @@ test_that("making the link table works", {
PomBaseID = c("SPBC460.01c", "SPCC5E4.03c"),
UniProtID = c("B5BP45", "O13282")))
expect_s3_class(dblt3, "data.frame")
expect_equal(ncol(dblt3), 4)
expect_equal(ncol(dblt3), 5)
expect_equal(nrow(dblt3), 2)
expect_named(dblt3, c("id", "UniProt", "AlphaFold", "ComplexPortal"))
expect_named(dblt3, c("id", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID"))
expect_equal(dblt3$id, factor(c("B5BP45", "O13282")))
expect_equal(dblt3$UniProt, c(
'<a href="https://www.uniprot.org/uniprot/B5BP45" target="_blank"> B5BP45</a>',
Expand All @@ -290,6 +311,10 @@ test_that("making the link table works", {
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=B5BP45" target="_blank"> B5BP45</a>',
'<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>'),
ignore_attr = TRUE)
expect_equal(dblt3$BioGRID, c(
'<a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>',
'<a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>'),
ignore_attr = TRUE)

## With Wormbase column
dblt4 <- makeDbLinkTable(
Expand All @@ -303,12 +328,14 @@ test_that("making the link table works", {
"WBGene00001330", "WBGene00001328"),
check.names = FALSE))
expect_s3_class(dblt4, "data.frame")
expect_equal(ncol(dblt4), 6)
expect_equal(ncol(dblt4), 7)
expect_equal(nrow(dblt4), 2)
expect_named(dblt4, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal", "WormBase"))
expect_named(dblt4, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID", "WormBase"))
expect_equal(grep(";", dblt4$UniProt), c(1, 2))
expect_equal(grep(";", dblt4$AlphaFold), c(1, 2))
expect_equal(grep(";", dblt4$ComplexPortal), c(1, 2))
expect_equal(grep(";", dblt4$BioGRID), c(1, 2))
expect_equal(grep(";", dblt4$WormBase), integer(0))
expect_equal(dblt4$gid, factor(c("eps-8", "epi-1")))
expect_equal(dblt4$pid, factor(c("Q7YTG1;O18250", "C1P641;C1P640")))
Expand All @@ -324,6 +351,10 @@ test_that("making the link table works", {
'<a href=\"https://www.ebi.ac.uk/complexportal/complex/search?query=Q7YTG1\" target=\"_blank\"> Q7YTG1</a>;<a href=\"https://www.ebi.ac.uk/complexportal/complex/search?query=O18250\" target=\"_blank\"> O18250</a>',
'<a href=\"https://www.ebi.ac.uk/complexportal/complex/search?query=C1P641\" target=\"_blank\"> C1P641</a>;<a href=\"https://www.ebi.ac.uk/complexportal/complex/search?query=C1P640\" target=\"_blank\"> C1P640</a>'),
ignore_attr = TRUE)
expect_equal(dblt4$BioGRID, c(
'<a href=\"https://thebiogrid.org/search.php?search=Q7YTG1&organism=all\" target=\"_blank\"> Q7YTG1</a>;<a href=\"https://thebiogrid.org/search.php?search=O18250&organism=all\" target=\"_blank\"> O18250</a>',
'<a href=\"https://thebiogrid.org/search.php?search=C1P641&organism=all\" target=\"_blank\"> C1P641</a>;<a href=\"https://thebiogrid.org/search.php?search=C1P640&organism=all\" target=\"_blank\"> C1P640</a>'),
ignore_attr = TRUE)
expect_equal(dblt4$WormBase, c(
'<a href="https://wormbase.org/species/c_elegans/gene/WBGene00001330" target="_blank"> WBGene00001330</a>',
'<a href="https://wormbase.org/species/c_elegans/gene/WBGene00001328" target="_blank"> WBGene00001328</a>'),
Expand All @@ -341,15 +372,18 @@ test_that("making the link table works", {
"WBGene00001330", "WBGene00001328"),
check.names = FALSE))
expect_s3_class(dblt5, "data.frame")
expect_equal(ncol(dblt5), 5)
expect_equal(ncol(dblt5), 6)
expect_equal(nrow(dblt5), 2)
expect_named(dblt5, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal"))
expect_named(dblt5, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID"))
expect_equal(grep(";", dblt5$UniProt), c(1, 2))
expect_equal(grep(";", dblt5$AlphaFold), c(1, 2))
expect_equal(grep(";", dblt5$ComplexPortal), c(1, 2))
expect_equal(grep(";", dblt5$BioGRID), c(1, 2))
expect_equal(dblt5$AlphaFold, dblt4$AlphaFold)
expect_equal(dblt5$UniProt, dblt4$UniProt)
expect_equal(dblt5$ComplexPortal, dblt4$ComplexPortal)
expect_equal(dblt5$BioGRID, dblt4$BioGRID)

## With Wormbase column, but missing conversion
dblt6 <- makeDbLinkTable(
Expand All @@ -362,18 +396,21 @@ test_that("making the link table works", {
WormBaseID = c("WBGene00001330", "WBGene00001328"),
check.names = FALSE))
expect_s3_class(dblt6, "data.frame")
expect_equal(ncol(dblt6), 6)
expect_equal(ncol(dblt6), 7)
expect_equal(nrow(dblt6), 2)
expect_named(dblt6, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal", "WormBase"))
expect_named(dblt6, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID", "WormBase"))
expect_equal(grep(";", dblt6$UniProt), c(1, 2))
expect_equal(grep(";", dblt6$AlphaFold), c(1, 2))
expect_equal(grep(";", dblt6$ComplexPortal), c(1, 2))
expect_equal(grep(";", dblt6$BioGRID), c(1, 2))
expect_equal(grep(";", dblt6$WormBase), integer(0))
expect_equal(dblt6$gid, factor(c("eps-8", "epi-1")))
expect_equal(dblt6$pid, factor(c("Q7YTG1;O18250", "C1P641;C1P640")))
expect_equal(dblt6$UniProt, dblt4$UniProt)
expect_equal(dblt6$AlphaFold, dblt4$AlphaFold)
expect_equal(dblt6$ComplexPortal, dblt4$ComplexPortal)
expect_equal(dblt6$BioGRID, dblt4$BioGRID)
expect_equal(dblt6$WormBase, dblt4$WormBase)

## With Wormbase column, but missing conversion (2)
Expand All @@ -386,18 +423,21 @@ test_that("making the link table works", {
WormBaseID = c("WBGene00001330"),
check.names = FALSE))
expect_s3_class(dblt7, "data.frame")
expect_equal(ncol(dblt7), 6)
expect_equal(ncol(dblt7), 7)
expect_equal(nrow(dblt7), 2)
expect_named(dblt7, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal", "WormBase"))
expect_named(dblt7, c("gid", "pid", "UniProt", "AlphaFold", "ComplexPortal",
"BioGRID", "WormBase"))
expect_equal(grep(";", dblt7$UniProt), c(1, 2))
expect_equal(grep(";", dblt7$AlphaFold), c(1, 2))
expect_equal(grep(";", dblt7$ComplexPortal), c(1, 2))
expect_equal(grep(";", dblt7$BioGRID), c(1, 2))
expect_equal(grep(";", dblt7$WormBase), integer(0))
expect_equal(dblt7$gid, factor(c("eps-8", "epi-1")))
expect_equal(dblt7$pid, factor(c("Q7YTG1;O18250", "C1P641;C1P640")))
expect_equal(dblt7$UniProt, dblt4$UniProt)
expect_equal(dblt7$AlphaFold, dblt4$AlphaFold)
expect_equal(dblt7$ComplexPortal, dblt4$ComplexPortal)
expect_equal(dblt7$BioGRID, dblt4$BioGRID)
expect_equal(dblt7$WormBase, c(dblt4$WormBase[1], ""),
ignore_attr = TRUE)

Expand Down

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