From 8c5f20dd97c08729dfd1090442a2f5a8a7e9f457 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 1 May 2024 15:27:51 -0400
Subject: [PATCH] chore: document

- also fix `density()` naming overlap
---
 NAMESPACE                                     |  2 +-
 R/package_imports.R                           |  2 +-
 man/createGiottoCosMxObject.Rd                |  6 +-
 man/createGiottoMerscopeObject.Rd             |  6 +-
 man/createGiottoXeniumObject.Rd               |  6 +-
 man/dot-createGiottoCosMxObject_aggregate.Rd  |  6 +-
 man/dot-createGiottoCosMxObject_all.Rd        |  6 +-
 ...dot-createGiottoCosMxObject_subcellular.Rd |  6 +-
 man/dot-createGiottoXeniumObject_aggregate.Rd |  6 +-
 ...ot-createGiottoXeniumObject_subcellular.Rd |  6 +-
 man/dot-load_cosmx_folder_aggregate.Rd        |  3 +-
 man/dot-load_cosmx_folder_subcellular.Rd      |  3 +-
 man/interpolateFeature.Rd                     | 95 +++++++++++++++++++
 man/load_merscope_folder.Rd                   |  3 +-
 man/load_xenium_folder.Rd                     |  3 +-
 15 files changed, 137 insertions(+), 22 deletions(-)
 create mode 100644 man/interpolateFeature.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 55032e2cd..7b3eb6556 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -493,7 +493,7 @@ import(GiottoUtils)
 import(GiottoVisuals)
 import(ggplot2)
 import(methods)
-import(stats)
+import(stats, except = density)
 import(utils)
 importClassesFrom(data.table,data.table)
 importFrom(GiottoClass,"activeFeatType<-")
diff --git a/R/package_imports.R b/R/package_imports.R
index 3aaaecefd..2e69841c7 100644
--- a/R/package_imports.R
+++ b/R/package_imports.R
@@ -3,7 +3,7 @@
 #' @import GiottoVisuals
 #' @import methods
 #' @import utils
-#' @import stats
+#' @rawNamespace import(stats, except = density)
 #' @import ggplot2
 #' @importClassesFrom data.table data.table
 #' @importFrom data.table setnames setorder setDT
diff --git a/man/createGiottoCosMxObject.Rd b/man/createGiottoCosMxObject.Rd
index 0362f0472..cbda75fe2 100644
--- a/man/createGiottoCosMxObject.Rd
+++ b/man/createGiottoCosMxObject.Rd
@@ -31,9 +31,11 @@ coordinates only. \code{'aggregate'} loads the provided aggregated expression ma
 
 \item{FOVs}{field of views to load (only affects subcellular data and images)}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/createGiottoMerscopeObject.Rd b/man/createGiottoMerscopeObject.Rd
index 960cbeeba..902b18197 100644
--- a/man/createGiottoMerscopeObject.Rd
+++ b/man/createGiottoMerscopeObject.Rd
@@ -51,9 +51,11 @@ NULL loads all FOVs (very slow)}
 
 \item{aggregate_stack_param}{params to pass to \code{\link{aggregateStacks}}}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 
diff --git a/man/createGiottoXeniumObject.Rd b/man/createGiottoXeniumObject.Rd
index 1c04cf0b8..7200c3346 100644
--- a/man/createGiottoXeniumObject.Rd
+++ b/man/createGiottoXeniumObject.Rd
@@ -46,9 +46,11 @@ a subcellular transcript detection (default = 20)}
 \item{key_list}{(advanced) list of grep-based keywords to split the subcellular
 feature detections by feature type. See details}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/dot-createGiottoCosMxObject_aggregate.Rd b/man/dot-createGiottoCosMxObject_aggregate.Rd
index f47f300db..1994734d6 100644
--- a/man/dot-createGiottoCosMxObject_aggregate.Rd
+++ b/man/dot-createGiottoCosMxObject_aggregate.Rd
@@ -12,11 +12,13 @@
 )
 }
 \arguments{
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 }
 \description{
 Load and create a CosMx Giotto object from aggregate info
diff --git a/man/dot-createGiottoCosMxObject_all.Rd b/man/dot-createGiottoCosMxObject_all.Rd
index 618a58814..df88e36c9 100644
--- a/man/dot-createGiottoCosMxObject_all.Rd
+++ b/man/dot-createGiottoCosMxObject_all.Rd
@@ -27,11 +27,13 @@
 
 \item{remove_unvalid_polygons}{remove unvalid polygons (default: TRUE)}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 }
 \description{
 Load and create a CosMx Giotto object from subcellular and aggregate info
diff --git a/man/dot-createGiottoCosMxObject_subcellular.Rd b/man/dot-createGiottoCosMxObject_subcellular.Rd
index 3e1c19c6b..c57640024 100644
--- a/man/dot-createGiottoCosMxObject_subcellular.Rd
+++ b/man/dot-createGiottoCosMxObject_subcellular.Rd
@@ -24,11 +24,13 @@
 
 \item{remove_unvalid_polygons}{remove unvalid polygons (default: TRUE)}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 }
 \description{
 Load and create a CosMx Giotto object from subcellular info
diff --git a/man/dot-createGiottoXeniumObject_aggregate.Rd b/man/dot-createGiottoXeniumObject_aggregate.Rd
index 4ed8cc25a..b77796716 100644
--- a/man/dot-createGiottoXeniumObject_aggregate.Rd
+++ b/man/dot-createGiottoXeniumObject_aggregate.Rd
@@ -14,9 +14,11 @@
 \arguments{
 \item{data_list}{list of data loaded by \code{.load_xenium_folder}}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/dot-createGiottoXeniumObject_subcellular.Rd b/man/dot-createGiottoXeniumObject_subcellular.Rd
index 03886fd2a..5072b5eb2 100644
--- a/man/dot-createGiottoXeniumObject_subcellular.Rd
+++ b/man/dot-createGiottoXeniumObject_subcellular.Rd
@@ -22,9 +22,11 @@ into separate giottoPoints objects by feat_type}
 \item{qv_threshold}{Minimum Phred-scaled quality score cutoff to be included as
 a subcellular transcript detection (default = 20)}
 
-\item{instructions}{list of instructions or output result from \code{\link[GiottoClass]{createGiottoInstructions}}}
+\item{instructions}{list of instructions or output result
+from \code{\link[GiottoClass]{createGiottoInstructions}}}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/dot-load_cosmx_folder_aggregate.Rd b/man/dot-load_cosmx_folder_aggregate.Rd
index 116cdeb8f..7ecd59161 100644
--- a/man/dot-load_cosmx_folder_aggregate.Rd
+++ b/man/dot-load_cosmx_folder_aggregate.Rd
@@ -7,7 +7,8 @@
 .load_cosmx_folder_aggregate(dir_items, cores, verbose = TRUE)
 }
 \arguments{
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/dot-load_cosmx_folder_subcellular.Rd b/man/dot-load_cosmx_folder_subcellular.Rd
index aff95f1a3..d79067d4b 100644
--- a/man/dot-load_cosmx_folder_subcellular.Rd
+++ b/man/dot-load_cosmx_folder_subcellular.Rd
@@ -9,7 +9,8 @@
 \arguments{
 \item{FOVs}{field of views to load (only affects subcellular data and images)}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/interpolateFeature.Rd b/man/interpolateFeature.Rd
new file mode 100644
index 000000000..325ceb5fd
--- /dev/null
+++ b/man/interpolateFeature.Rd
@@ -0,0 +1,95 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kriging.R
+\name{interpolateFeature}
+\alias{interpolateFeature}
+\alias{interpolateFeature,giotto,missing-method}
+\alias{interpolateFeature,spatLocsObj,data.frame-method}
+\title{Spatial feature interpolation}
+\usage{
+\S4method{interpolateFeature}{giotto,missing}(
+  x,
+  spat_unit = NULL,
+  feat_type = NULL,
+  feats,
+  spatvalues_params = list(),
+  spat_loc_name = "raw",
+  ext = NULL,
+  buffer = 50,
+  name_fmt = "\%s",
+  savedir = file.path(getwd(), "interp_rasters"),
+  overwrite = FALSE,
+  verbose = NULL,
+  ...
+)
+
+\S4method{interpolateFeature}{spatLocsObj,data.frame}(
+  x,
+  y,
+  ext = NULL,
+  buffer = 50,
+  rastersize = 500,
+  name_fmt = "\%s",
+  savedir = file.path(getwd(), "interp_rasters"),
+  overwrite = FALSE,
+  ...
+)
+}
+\arguments{
+\item{x}{object containing coordinates to use interpolation with}
+
+\item{spat_unit}{(optional) spatial unit to use}
+
+\item{feat_type}{(optional) feature type to use}
+
+\item{feats}{character vector. Features to interpolate from the `giotto`
+object}
+
+\item{spatvalues_params}{list. Additional list of parameters to pass to
+[spatValues()] to help with data retrieval from `giotto` object}
+
+\item{spat_loc_name}{character. Name of spatial locations to use. Values to
+be interpolated are spatially mapped to these locations by cell_ID.}
+
+\item{ext}{`SpatExtent`. (optional) extent across which to apply the
+interpolation. If not provided, will default to the extent of the spatLocsObj
+expanded by the value of `buffer`. It can be helpful to set this as the
+extent of any polygons that will be used in aggregation.}
+
+\item{buffer}{numeric. (optional) default buffer to expand derived extent by
+if `ext` is not provided.}
+
+\item{name_fmt}{character. sprintf fmt to apply to `feats` when naming the
+resulting interpolation `giottoLargeImage` objects. Default is no change.}
+
+\item{savedir}{character. Output directory. Default is a new `interp_rasters`
+folder in working directory.}
+
+\item{overwrite}{logical. Whether raster outputs should be overwritten if
+the same `filename` is provided.}
+
+\item{verbose}{be verbose}
+
+\item{...}{additional params to pass downstream methods}
+
+\item{y}{data.frame-like. Values for interpolation. Must also have a
+`cell_ID` column and that matches with `x`.}
+
+\item{rastersize}{numeric. Length of major axis in px of interpolation
+raster to create.}
+
+\item{name}{name of interpolation `giottoLargeImage` to generate}
+
+\item{filename}{character. Output filename. Default is \[`name`\].tif within
+the working directory.}
+}
+\value{
+`giotto` method returns a `giotto` object with newly made appended
+feature interpolation rasters as `giottoLargeImages`\cr
+}
+\description{
+Spatial feature interpolation
+}
+\details{
+The data.frame method returns a `giottoLargeImage` linked to an interpolated
+raster that is written to disk as GeoTIFF.
+}
diff --git a/man/load_merscope_folder.Rd b/man/load_merscope_folder.Rd
index 42571cf25..6e9b9a54c 100644
--- a/man/load_merscope_folder.Rd
+++ b/man/load_merscope_folder.Rd
@@ -38,7 +38,8 @@
 \item{data_to_use}{which of either the 'subcellular' or 'aggregate' information
 to use for object creation}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }
diff --git a/man/load_xenium_folder.Rd b/man/load_xenium_folder.Rd
index af16eff91..3ed9d4603 100644
--- a/man/load_xenium_folder.Rd
+++ b/man/load_xenium_folder.Rd
@@ -55,7 +55,8 @@ expression matrix}
 
 \item{gene_column_index}{which column from the features or genes .tsv file to use for row ids}
 
-\item{cores}{how many cores or threads to use to read data if paths are provided}
+\item{cores}{how many cores or threads to use to read data if paths are
+provided}
 
 \item{verbose}{be verbose when building Giotto object}
 }