-
Notifications
You must be signed in to change notification settings - Fork 17
/
SpatialExperiment.R
377 lines (363 loc) · 14.2 KB
/
SpatialExperiment.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
#' @name SpatialExperiment
#'
#' @title The SpatialExperiment class
#'
#' @aliases
#' SpatialExperiment
#' SpatialExperiment-class
#'
#' @description
#' The \code{SpatialExperiment} class is designed to represent spatially
#' resolved transcriptomics (ST) data. It inherits from the
#' \code{\link{SingleCellExperiment}} class and is used in the same manner. In
#' addition, the class supports storage of spatial information via
#' \code{\link{spatialCoords}} and storage of images via \code{\link{imgData}}.
#'
#' @param ... Arguments passed to the \code{\link{SingleCellExperiment}}
#' constructor to fill the slots of the base class.
#' @param sample_id A \code{character} sample identifier, which matches the
#' \code{sample_id} in \code{\link{imgData}}. The \code{sample_id} will also
#' be stored in a new column in \code{\link{colData}}, if not already present.
#' Default = \code{sample01}.
#' @param spatialCoordsNames A \code{character} vector of column names from
#' \code{\link{colData}} containing spatial coordinates, which will be
#' accessible with \code{\link{spatialCoords}}. Alternatively, the
#' \code{spatialCoords} argument may be provided. If both are provided,
#' \code{spatialCoordsNames} is given precedence, and a warning is returned.
#' Default = \code{c("x", "y")}.
#' @param spatialCoords A numeric matrix containing columns of spatial
#' coordinates, which will be accessible with \code{\link{spatialCoords}}.
#' Alternatively, \code{spatialCoordsNames} may be provided. If both are
#' provided, \code{spatialCoordsNames} is given precedence, and a warning is
#' returned.
#' @param scaleFactors Optional scale factors associated with the image(s). This
#' can be provided as a numeric value, numeric vector, list, or file path to a
#' JSON file for the 10x Genomics Visium platform. For 10x Genomics Visium,
#' the correct scale factor will automatically be selected depending on the
#' resolution of the image from \code{imageSources}. Default = \code{1}.
#' @param imgData Optional \code{\link{DataFrame}} containing the image data.
#' Alternatively, this can be built from the arguments \code{imageSources} and
#' \code{image_id} (see Details).
#' @param imageSources Optional file path(s) or URL(s) for one or more image
#' sources.
#' @param image_id Optional character vector (same length as
#' \code{imageSources}) containing unique image identifiers.
#' @param loadImage Logical indicating whether to load image into memory.
#' Default = \code{FALSE}.
#' @param spatialDataNames (Deprecated) A \code{character} vector of column
#' names from \code{\link{colData}} to include in \code{\link{spatialData}}.
#' Alternatively, the \code{spatialData} argument may be provided. If both are
#' provided, \code{spatialDataNames} is given precedence, and a warning is
#' returned. (Note: \code{spatialData} and \code{spatialDataNames} have been
#' deprecated; \code{colData} and \code{spatialCoords} should be used for all
#' columns. The arguments have been retained for backward compatibility but
#' may be removed in the future.)
#' @param spatialData (Deprecated) A \code{\link{DataFrame}} containing columns
#' to store in \code{\link{spatialData}}, which must contain at least the
#' columns of spatial coordinates. Alternatively, \code{spatialDataNames} may
#' be provided. If both are provided, \code{spatialDataNames} is given
#' precedence, and a warning is returned. (Note: \code{spatialData} and
#' \code{spatialDataNames} have been deprecated; \code{colData} and
#' \code{spatialCoords} should be used for all columns. The arguments have
#' been retained for backward compatibility but may be removed in the future.)
#'
#' @details
#' In this class, rows represent genes, and columns represent spots (for
#' spot-based ST platforms) or cells (for molecule-based ST platforms). As for
#' \code{\link{SingleCellExperiment}}, \code{counts} and \code{logcounts} can be
#' stored in the \code{\link{assays}} slot, and row and column metadata in
#' \code{\link{rowData}} and \code{\link{colData}}. For molecule-based ST data,
#' the additional measurements per molecule per cell can be stored in a
#' \code{BumpyMatrix}-formatted \code{assay} named \code{\link{molecules}}.
#'
#' The additional arguments in the constructor documented above (e.g.
#' \code{spatialCoords}, \code{imgData}, and others) represent the extensions to
#' the \code{\link{SingleCellExperiment}} class to store associated spatial and
#' imaging information for ST data.
#'
#' The constructor expects \code{colData} to contain a column named
#' \code{sample_id}. If this is not present, it will assign the value from the
#' \code{sample_id} argument. If the \code{imgData} argument is provided, the
#' constructor expects the \code{\link{imgData}} \code{\link{DataFrame}} to
#' already be built. Otherwise, it will build it from the \code{imageSources}
#' and (optional) \code{image_id} arguments. If \code{image_id} is not provided,
#' this will be assumed from \code{sample_id} and \code{imageSources} instead.
#' To combine multiple samples within a single object, see
#' \code{\link{combine}}.
#'
#' For 10x Genomics Visium datasets, the function \code{\link{read10xVisium}}
#' can be used to load data and create a \code{SpatialExperiment} object
#' directly from Space Ranger output files.
#'
#' @seealso
#' \code{?"\link{SpatialExperiment-methods}"}, which includes:
#' \code{\link{spatialCoords}}, \code{\link{spatialCoordsNames}},
#' \code{\link{imgData}}, \code{\link{scaleFactors}}
#'
#' \code{?"\link{SpatialExperiment-assays}"}, which includes:
#' \code{\link{molecules}}
#'
#' \code{?"\link{SpatialExperiment-colData}"}
#'
#' \code{?"\link{SpatialExperiment-combine}"}
#'
#' \code{?"\link{SpatialExperiment-subset}"}
#'
#' \code{?"\link{SpatialExperiment-misc}"}
#'
#' \code{\link{readImgData}}
#'
#' \code{?"\link{imgData-methods}"}
#'
#' \code{\link{SpatialImage}}
#'
#' \code{\link{read10xVisium}}
#'
#' @author Dario Righelli and Helena L. Crowell
#'
#' @return A \code{SpatialExperiment} object.
#'
#' @examples
#' #########################################################
#' # Example 1: Spot-based ST (10x Visium) using constructor
#' #########################################################
#'
#' dir <- system.file(
#' file.path("extdata", "10xVisium", "section1", "outs"),
#' package = "SpatialExperiment")
#'
#' # read in counts
#' fnm <- file.path(dir, "raw_feature_bc_matrix")
#' sce <- DropletUtils::read10xCounts(fnm)
#'
#' # read in image data
#' img <- readImgData(
#' path = file.path(dir, "spatial"),
#' sample_id="foo")
#'
#' # read in spatial coordinates
#' fnm <- file.path(dir, "spatial", "tissue_positions_list.csv")
#' xyz <- read.csv(fnm, header = FALSE,
#' col.names = c(
#' "barcode", "in_tissue", "array_row", "array_col",
#' "pxl_row_in_fullres", "pxl_col_in_fullres"))
#'
#' # construct observation & feature metadata
#' rd <- S4Vectors::DataFrame(
#' symbol = rowData(sce)$Symbol)
#'
#' # construct 'SpatialExperiment'
#' (spe <- SpatialExperiment(
#' assays = list(counts = assay(sce)),
#' rowData = rd,
#' colData = DataFrame(xyz),
#' spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
#' imgData = img,
#' sample_id = "foo"))
#'
#' #############################################################
#' # Example 2: Spot-based ST (10x Visium) using 'read10xVisium'
#' #############################################################
#'
#' # see ?read10xVisium for details
#' example(read10xVisium)
#'
#' ##############################
#' # Example 3: Molecule-based ST
#' ##############################
#'
#' # create simulated data
#' n <- 1000; ng <- 50; nc <- 20
#' # sample xy-coordinates in [0,1]
#' x <- runif(n)
#' y <- runif(n)
#' # assign each molecule to some gene-cell pair
#' gs <- paste0("gene", seq(ng))
#' cs <- paste0("cell", seq(nc))
#' gene <- sample(gs, n, TRUE)
#' cell <- sample(cs, n, TRUE)
#' # construct data.frame of molecule coordinates
#' df <- data.frame(gene, cell, x, y)
#'
#' # (assure gene & cell are factor so that
#' # missing observations aren't dropped)
#' df$gene <- factor(df$gene, gs)
#' df$cell <- factor(df$cell, cs)
#'
#' # construct BumpyMatrix
#' mol <- BumpyMatrix::splitAsBumpyMatrix(
#' df[, c("x", "y")],
#' row = df$gene, column = df$cell)
#'
#' # get count matrix
#' y <- with(df, table(gene, cell))
#' y <- as.matrix(unclass(y))
#'
#' # construct SpatialExperiment
#' (spe_mol <- SpatialExperiment(
#' assays = list(
#' counts = y,
#' molecules = mol)))
NULL
#' @importFrom S4Vectors DataFrame
#' @importFrom SingleCellExperiment SingleCellExperiment
#' @export
SpatialExperiment <- function(...,
sample_id="sample01",
spatialCoordsNames=NULL,
spatialCoords=NULL,
scaleFactors=1,
imageSources=NULL,
image_id=NULL,
loadImage=FALSE,
imgData=NULL,
spatialDataNames=NULL,
spatialData=NULL) {
sce <- SingleCellExperiment(...)
spe <- .sce_to_spe(sce=sce,
sample_id=sample_id,
spatialCoordsNames=spatialCoordsNames,
spatialCoords=spatialCoords,
scaleFactors=scaleFactors,
imageSources=imageSources,
image_id=image_id,
loadImage=loadImage,
imgData=imgData,
spatialDataNames=spatialDataNames,
spatialData=spatialData)
return(spe)
}
#' @importFrom methods new
#' @importFrom S4Vectors DataFrame
#' @importFrom SingleCellExperiment int_metadata<-
.sce_to_spe <- function(sce,
sample_id="sample01",
spatialCoordsNames=NULL,
spatialCoords=NULL,
scaleFactors=1,
imageSources=NULL,
image_id=NULL,
loadImage=TRUE,
imgData=NULL,
spatialDataNames=NULL,
spatialData=NULL) {
old <- S4Vectors:::disableValidity()
if (!isTRUE(old)) {
S4Vectors:::disableValidity(TRUE)
on.exit(S4Vectors:::disableValidity(old))
}
if (is.null(sce$sample_id)) {
stopifnot(
is.character(sample_id),
any(length(sample_id) == c(1, ncol(sce))))
if (ncol(sce) == 0)
sample_id <- character()
sce$sample_id <- sample_id
} else {
if (!is.character(sce$sample_id))
sce$sample_id <- as.character(sce$sample_id)
sample_id <- unique(sce$sample_id)
}
if (!is.null(spatialData) || !is.null(spatialDataNames)) {
.msg_spatialData()
}
spe <- new("SpatialExperiment", sce)
# in the following code chunk, we give precedence
# to spatialData/CoordsNames over spatialData/Coords
# where spatialDataNames should be in colData,
# and spatialCoordsNames can be in both colData and spatialData
# if both spatialData/Coords and -Names are supplied
# we give an informative warning notifying the user
# that spatialData/CoordsNames will be used
msg <- function(.) message(sprintf(
"Both '%s' and '%sNames' have been supplied;\nusing '%s'. ", ., ., .),
"Set either to NULL to suppress this message.")
if (!is.null(spatialCoordsNames)) {
stopifnot(is.character(spatialCoordsNames),
all(spatialCoordsNames %in% names(colData(spe)))
|| all(spatialCoordsNames %in% names(spatialData)))
if (!is.null(spatialCoords))
msg("spatialCoords")
if (all(spatialCoordsNames %in% names(colData(spe)))) {
i <- spatialCoordsNames
j <- setdiff(names(colData(spe)), i)
spatialCoords(spe) <- as.matrix(colData(spe)[i])
colData(spe) <- colData(spe)[j]
} else {
i <- spatialCoordsNames
j <- setdiff(names(spatialData), i)
spatialCoords(spe) <- as.matrix(spatialData[i])
spatialData <- spatialData[j]
}
} else if (!is.null(spatialCoords)) {
stopifnot(
is.matrix(spatialCoords),
is.numeric(spatialCoords),
nrow(spatialCoords) == ncol(spe))
spatialCoords(spe) <- spatialCoords
} else {
spatialCoords(spe) <- NULL
}
if (!is.null(spatialDataNames)) {
stopifnot(
is.character(spatialDataNames),
spatialDataNames %in% names(colData(spe)))
if (!is.null(spatialData))
msg("spatialData")
i <- spatialDataNames
j <- setdiff(names(colData(spe)), i)
spd <- colData(spe)[i]
colData(spe) <- colData(spe)[j]
spatialData(spe) <- spd
} else if (!is.null(spatialData)) {
stopifnot(
is(spatialData, "DFrame"),
nrow(spatialData) == ncol(spe))
spatialData(spe) <- spatialData
} else {
spatialData(spe) <- NULL
}
if (!is.null(imgData)) {
stopifnot(imgData$sample_id %in% spe$sample_id)
imgData(spe) <- imgData
} else if (!is.null(imageSources) ){
if (is.null(image_id)) {
image_id <- sub("(.*)\\..*$", "\\1", basename(imageSources))
image_id <- paste0(sample_id, "_", image_id, seq_along(imageSources))
} else {
stopifnot(length(image_id) != length(imageSources))
}
for (i in seq_along(imageSources)) {
scaleFactor <- .get_scaleFactor(scaleFactors, imageSources[i])
spe <- addImg(spe,
imageSource=imageSources[i], scaleFactor=scaleFactor,
sample_id=sample_id[i], image_id=image_id[i], load=loadImage)
}
} else {
imgData(spe) <- NULL
}
return(spe)
}
#' @importFrom rjson fromJSON
.get_scaleFactor <- function(scaleFactors, imageSource=NULL) {
scf <- scaleFactors
if (is.numeric(scf))
return(scf)
if (!is.list(scf)) {
if (!(is.character(scaleFactors) && grepl("\\.json$", scaleFactors)))
stop("scaleFactors should be numeric, a list or JSON file.")
scf <- fromJSON(file=scaleFactors)
}
if (!is.null(imageSource)) {
img_fnm <- basename(imageSource)
if (grepl("lowres", img_fnm)) {
scf <- scf$tissue_lowres_scalef
} else if (grepl("hires", img_fnm)) {
scf <- scf$tissue_lowres_scalef
} else {
stop("Couldn't match input imageSources and scaleFactors; please",
" provide a numeric value or a list of scaleFactors instead.")
}
}
return(scf)
}