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@@ -68,8 +68,64 @@ createRasterizedObject <- function(input, out, name) { | |
| } | ||
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| #' rasterizeGeneExpression | ||
| #' @export | ||
| #' | ||
| #' @description Function to rasterize feature x observation matrix in spatially-resolved | ||
| #' omics data represented as Seurat objects. | ||
| #' | ||
| #' @description This function assumes that the input is provided as a \code{Seurat} | ||
| #' object or a \code{list} of \code{Seurat} objects. | ||
| #' | ||
| #' @param input \code{Seurat} object or \code{list}: Input data represented as a | ||
| #' \code{Seurat} object or \code{list} of \code{Seurat} objects. | ||
| #' | ||
| #' @param assay_name (character) Assay in Seurat object to use. If not specified, selects the default assay | ||
| #' | ||
| #' @param image (character) Image in Seurat object to use. If not specified, defaults to the first image available associated with the assay | ||
| #' | ||
| #' @param slot (character) Slot in Seurat assay to use. If not specified, defaults to counts | ||
| #' | ||
| #' @param resolution \code{integer} or \code{double}: Resolution refers to the side | ||
| #' length of each pixel for square pixels and the distance between opposite edges | ||
| #' of each pixel for hexagonal pixels. The unit of this parameter is assumed to | ||
| #' be the same as the unit of spatial coordinates of the input data. | ||
| #' | ||
| #' @param square \code{logical}: If TRUE (default), rasterize into square pixels. If FALSE, rasterize into hexagonal pixels, although not supported by Seurat plotting functions. | ||
| #' | ||
| #' @param fun \code{character}: If "mean", pixel value for each pixel | ||
| #' would be the proportion of each cell type based on the one-hot-encoded cell type | ||
| #' labels for all cells within the pixel. If "sum", pixel value for each pixel would | ||
| #' be the number of cells of each cell type based on the one-hot-encoded cell type | ||
| #' labels for all cells within the pixel. | ||
| #' | ||
| #' @param n_threads \code{integer}: Number of threads for parallelization. Default = 1. | ||
| #' Inputting this argument when the \code{BPPARAM} argument is missing would set parallel | ||
| #' exeuction back-end to be \code{BiocParallel::MulticoreParam(workers = n_threads)}. | ||
| #' We recommend setting this argument to be the number of cores available | ||
| #' (\code{parallel::detectCores(logical = FALSE)}). If \code{BPPARAM} argument is | ||
| #' not missing, the \code{BPPARAM} argument would override \code{n_threads} argument. | ||
| #' | ||
| #' @param BPPARAM \code{BiocParallelParam}: Optional additional argument for parallelization. | ||
| #' This argument is provided for advanced users of \code{BiocParallel} for further | ||
| #' flexibility for setting up parallel-execution back-end. Default is NULL. If | ||
| #' provided, this is assumed to be an instance of \code{BiocParallelParam}. | ||
| #' | ||
| #' @param verbose \code{logical}: Whether to display verbose output or warning. Default is FALSE | ||
| #' | ||
| #' @return If the input was given as \code{Seurat} object, the output is returned | ||
| #' as a new \code{Seurat} object with \code{assay} slot containing the | ||
| #' feature (cell types) x observations (pixels) matrix (dgCmatrix), \code{field of view} | ||
| #' slot containing spatial x,y coordinates of pixel centroids, and meta data for pixels | ||
| #' (number of cells that were aggregated in each pixel, | ||
| #' cell IDs of cells that were aggregated in each pixel, pixel type based on the | ||
| #' \code{square} argument, pixel resolution based on the \code{resolution} argument. | ||
| #' If the input was provided as \code{list} of \code{Seurat} objects, the output is | ||
| #' returned as a new \code{list} of \code{Seurat} objects containing information described | ||
| #' above for corresponding \code{Seurat} object. | ||
| #' | ||
| #' @importFrom SEraster rasterizeMatrix | ||
| #' @importFrom Matrix colSums | ||
| #' | ||
| #' @export | ||
| rasterizeGeneExpression <- function( | ||
| input, | ||
| assay_name = NULL, | ||
|
|
@@ -171,6 +227,54 @@ rasterizeGeneExpression <- function( | |
| #' @description This function assumes that the input is provided as a \code{Seurat object} | ||
| #' object or a \code{list} of \code{Seurat} objects. | ||
| #' | ||
| #' @param input \code{Seurat} object or \code{list}: Input data represented as a | ||
| #' \code{Seurat} object or \code{list} of \code{Seurat} objects. | ||
| #' | ||
| #' @param col_name (character) Name of metadata column to rasterize on | ||
| #' | ||
| #' @param assay_name (character) Assay in Seurat object to use. If not specified, selects the default assay | ||
| #' | ||
| #' @param image (character) Image in Seurat object to use. If not specified, defaults to the first image available associated with the assay | ||
| #' | ||
| #' @param resolution \code{integer} or \code{double}: Resolution refers to the side | ||
| #' length of each pixel for square pixels and the distance between opposite edges | ||
| #' of each pixel for hexagonal pixels. The unit of this parameter is assumed to | ||
| #' be the same as the unit of spatial coordinates of the input data. | ||
| #' | ||
| #' @param square \code{logical}: If TRUE (default), rasterize into square pixels. If FALSE, rasterize into hexagonal pixels, although not supported by Seurat plotting functions. | ||
| #' | ||
| #' @param fun \code{character}: If "mean", pixel value for each pixel | ||
| #' would be the proportion of each cell type based on the one-hot-encoded cell type | ||
| #' labels for all cells within the pixel. If "sum", pixel value for each pixel would | ||
| #' be the number of cells of each cell type based on the one-hot-encoded cell type | ||
| #' labels for all cells within the pixel. | ||
| #' | ||
| #' @param n_threads \code{integer}: Number of threads for parallelization. Default = 1. | ||
| #' Inputting this argument when the \code{BPPARAM} argument is missing would set parallel | ||
| #' exeuction back-end to be \code{BiocParallel::MulticoreParam(workers = n_threads)}. | ||
| #' We recommend setting this argument to be the number of cores available | ||
| #' (\code{parallel::detectCores(logical = FALSE)}). If \code{BPPARAM} argument is | ||
| #' not missing, the \code{BPPARAM} argument would override \code{n_threads} argument. | ||
| #' | ||
| #' @param BPPARAM \code{BiocParallelParam}: Optional additional argument for parallelization. | ||
| #' This argument is provided for advanced users of \code{BiocParallel} for further | ||
| #' flexibility for setting up parallel-execution back-end. Default is NULL. If | ||
| #' provided, this is assumed to be an instance of \code{BiocParallelParam}. | ||
| #' | ||
| #' @param verbose \code{logical}: Whether to display verbose output or warning. Default is FALSE | ||
| #' | ||
| #' @return If the input was given as \code{Seurat} object, the output is returned | ||
| #' as a new \code{Seurat} object with \code{assay} slot containing the | ||
| #' feature (cell types) x observations (pixels) matrix (dgCmatrix), \code{field of view} | ||
| #' slot containing spatial x,y coordinates of pixel centroids, and meta data for pixels | ||
| #' (number of cells that were aggregated in each pixel, | ||
| #' cell IDs of cells that were aggregated in each pixel, pixel type based on the | ||
| #' \code{square} argument, pixel resolution based on the \code{resolution} argument. | ||
| #' If the input was provided as \code{list} of \code{Seurat} objects, the output is | ||
| #' returned as a new \code{list} of \code{Seurat} objects containing information described | ||
| #' above for corresponding \code{Seurat} object. | ||
| #' | ||
| #' @importFrom SEraster rasterizeMatrix | ||
| #' @importFrom Matrix sparse.model.matrix t colSums | ||
| #' | ||
| #' @export | ||
|
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@@ -281,6 +385,21 @@ rasterizeCellType <- function( | |
| #' all \code{Seurat} objects will be rotated around a common midrange | ||
| #' point computed based on combined x,y coordinates. | ||
| #' | ||
| #' @param input \code{Seurat} object or \code{list}: Input data represented as a | ||
| #' \code{Seurat} object or \code{list} of \code{Seurat} objects. | ||
| #' | ||
| #' @param n_perm \code{integer}: Number of permutations. Default = 1. This number is used to compute the angles at which the input is rotated at. | ||
| #' | ||
| #' @param verbose \code{logical}: Whether to display verbose output or warning. Default is FALSE. | ||
| #' | ||
| #' @return If the input was given as \code{Seurat} object, the output is returned | ||
| #' as a \code{list} of \code{n_perm} \code{Seurat} objects. Each \code{SpatialExperiment} | ||
| #' object has an updated field of view containing the spatial x,y coordinates | ||
| #' rotated at a corresponding angle. \code{assay} and metadata are inherited. | ||
| #' If the input was given as \code{list} of \code{Seurat} objects, | ||
| #' the output is returned as a new \code{list} of \code{length(input)} * \code{n_perm} | ||
| #' \code{Seurat} objects. | ||
| #' | ||
| #' @importFrom rearrr rotate_2d midrange | ||
| #' | ||
| #' @export | ||
|
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@@ -318,9 +437,8 @@ permutateByRotation <- function(input, n_perm = 1, verbose = FALSE) { | |
| image_name <- Images(spe, assay = assay_name)[[1]] | ||
| class <- class(spe[[image_name]]) | ||
|
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||
| if (class == 'VisiumV1') { | ||
| input <- updateVisiumV1(spe, pos_rotated, assay_name, angle, image_name) | ||
| } else if (class == 'VisiumV2') { | ||
| if (class == 'VisiumV1' || class == 'VisiumV2') { | ||
| message("Returning objects as VisiumV2 classes...") | ||
| input <- updateVisiumV2(spe, pos_rotated, assay_name, angle, image_name) | ||
| } else if (class == 'FOV') { | ||
| input <- updateFOV(spe, pos_rotated, assay_name, angle, image_name) | ||
|
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@@ -346,9 +464,8 @@ permutateByRotation <- function(input, n_perm = 1, verbose = FALSE) { | |
|
|
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| class <- class(input[[image_name]]) | ||
|
|
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| if (class == 'VisiumV1') { | ||
| output <- updateVisiumV1(input, pos_rotated, assay_name, angle, image_name) | ||
| } else if (class == 'VisiumV2') { | ||
| if (class == 'VisiumV1' || class == 'VisiumV2') { | ||
| message("Returning objects as VisiumV2 classes...") | ||
| output <- updateVisiumV2(input, pos_rotated, assay_name, angle, image_name) | ||
| } else if (class == 'FOV') { | ||
| output <- updateFOV(input, pos_rotated, assay_name, angle, image_name) | ||
|
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@@ -359,33 +476,6 @@ permutateByRotation <- function(input, n_perm = 1, verbose = FALSE) { | |
| } | ||
| } | ||
|
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| #' @keyword internal | ||
| #' | ||
| updateVisiumV1 <- function(input, pos_rotated, assay_name, angle, image_name) { | ||
| scale.use <- ScaleFactors(input[[image_name]])[['lowres']] | ||
| pos_old <- slot(input[[image_name]], name = "coordinates") | ||
| pos_new <- as.data.frame(cbind(tissue = pos_old$tissue, | ||
| row = pos_rotated$x, | ||
| col = pos_rotated$y, | ||
| imagerow = ceiling(pos_rotated$x / scale.use), | ||
| imagecol = ceiling(pos_rotated$y / scale.use))) | ||
| rownames(pos_new) <- rownames(pos_rotated) | ||
| input_fov <- input[[image_name]] | ||
|
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| visium.fov <- new( | ||
| Class = "VisiumV1", | ||
| coordinates = pos_new, | ||
| assay = assay_name, | ||
| key = paste0("rotated", angle, "_"), | ||
| image = rotate(input_fov@image, angle, pos_new), | ||
| scale.factors = [email protected], | ||
| spot.radius = [email protected] | ||
| ) | ||
| input[[image_name]] <- NULL | ||
| input@images[[paste0("rotated", angle)]] <- visium.fov | ||
| return(input) | ||
| } | ||
|
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| #' @keyword internal | ||
| #' | ||
| updateVisiumV2 <- function(input, pos_rotated, assay_name, angle, image_name) { | ||
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