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Fix for Join Giotto Objects with Polygon information #338

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Fix for Join Giotto Objects with Polygon information #338

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21 changes: 18 additions & 3 deletions R/join.R
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@
verbose = FALSE) {
# NSE vars
sdimz <- cell_ID <- sdimx <- sdimy <- name <- NULL

core_units <- c("cell", "spot")
n_gobjects <- length(gobject_list)
gobj_idx <- seq_len(n_gobjects)

Expand Down Expand Up @@ -538,7 +538,18 @@
set_defaults = FALSE
)

cx[][["list_ID"]] <- gname
if (spat_unit %in% core_units) {
if (nrow(cx[]) == 0) {
stop(sprintf("Core spat_unit '%s' has 0 rows, object is invalid.", spat_unit))

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Code scanning / lintr

Lines should not be more than 80 characters. This line is 102 characters. Note

Lines should not be more than 80 characters. This line is 102 characters.
}
} else {
if (nrow(cx[]) == 0) {
next # polygon units
}
}

cx[][["list_ID"]] <- rep(gname, nrow(cx[]))
#cx[][["list_ID"]] <- gname

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Remove commented code.
cx[][["cell_ID"]] <- paste0(gname, "-", cx[][["cell_ID"]])
gobj <- setGiotto(gobj, cx,
initialize = FALSE, verbose = FALSE
Expand Down Expand Up @@ -697,7 +708,11 @@
return_giottoPolygon = TRUE
)
spat_information_vector <- gpoly[]
spat_information_centroids <- centroids(gpoly)
spat_information_centroids <- tryCatch(
centroids(gpoly),

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no visible global function definition for 'centroids' Warning

no visible global function definition for 'centroids'
error = function(e) NULL
)
# spat_information_centroids <- centroids(gpoly)

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Code scanning / lintr

Remove commented code. Note

Remove commented code.

savelist_vector[[gobj_i]] <- spat_information_vector
savelist_centroids[[gobj_i]] <- spat_information_centroids
Expand Down
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