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Merge branch 'dev' of github.com:KrishnaswamyLab/MAGIC into dev
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@scottgigante
scottgigante committed Mar 10, 2021
2 parents 91eade0 + f751df4 commit 212d803
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260 changes: 125 additions & 135 deletions Rmagic/R/magic.R
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Original file line number Diff line number Diff line change
Expand Up @@ -55,80 +55,74 @@
#'
#' @examples
#' if (pymagic_is_available()) {
#'
#' data(magic_testdata)
#'
#' # Run MAGIC
#' data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))
#' summary(data_magic)
#' ## CDH1 VIM ZEB1
#' ## Min. :0.4303 Min. :3.854 Min. :0.01111
#' ## 1st Qu.:0.4444 1st Qu.:3.947 1st Qu.:0.01145
#' ## Median :0.4462 Median :3.964 Median :0.01153
#' ## Mean :0.4461 Mean :3.965 Mean :0.01152
#' ## 3rd Qu.:0.4478 3rd Qu.:3.982 3rd Qu.:0.01160
#' ## Max. :0.4585 Max. :4.127 Max. :0.01201
#'
#' # Plot the result with ggplot2
#' if (require(ggplot2)) {
#' ggplot(data_magic) +
#' geom_point(aes(x=VIM, y=CDH1, color=ZEB1))
#' }
#'
#' # Run MAGIC again returning all genes
#' # We use the last run as initialization
#' data_magic <- magic(magic_testdata, genes="all_genes", init=data_magic)
#' # Extract the smoothed data matrix to use in downstream analysis
#' data_smooth <- as.matrix(data_magic)
#'
#' data(magic_testdata)
#'
#' # Run MAGIC
#' data_magic <- magic(magic_testdata, genes = c("VIM", "CDH1", "ZEB1"))
#' summary(data_magic)
#' ## CDH1 VIM ZEB1
#' ## Min. :0.4303 Min. :3.854 Min. :0.01111
#' ## 1st Qu.:0.4444 1st Qu.:3.947 1st Qu.:0.01145
#' ## Median :0.4462 Median :3.964 Median :0.01153
#' ## Mean :0.4461 Mean :3.965 Mean :0.01152
#' ## 3rd Qu.:0.4478 3rd Qu.:3.982 3rd Qu.:0.01160
#' ## Max. :0.4585 Max. :4.127 Max. :0.01201
#'
#' # Plot the result with ggplot2
#' if (require(ggplot2)) {
#' ggplot(data_magic) +
#' geom_point(aes(x = VIM, y = CDH1, color = ZEB1))
#' }
#'
#' # Run MAGIC again returning all genes
#' # We use the last run as initialization
#' data_magic <- magic(magic_testdata, genes = "all_genes", init = data_magic)
#' # Extract the smoothed data matrix to use in downstream analysis
#' data_smooth <- as.matrix(data_magic)
#' }
#'
#' if (pymagic_is_available() && require(Seurat)) {
#' data(magic_testdata)
#'
#' data(magic_testdata)
#'
#' # Create a Seurat object
#' seurat_object <- CreateSeuratObject(counts = t(magic_testdata), assay="RNA")
#' seurat_object <- NormalizeData(object = seurat_object)
#' seurat_object <- ScaleData(object = seurat_object)
#'
#' # Run MAGIC and reset the active assay
#' seurat_object <- magic(seurat_object)
#' seurat_object@active.assay = "MAGIC_RNA"
#' # Create a Seurat object
#' seurat_object <- CreateSeuratObject(counts = t(magic_testdata), assay = "RNA")
#' seurat_object <- NormalizeData(object = seurat_object)
#' seurat_object <- ScaleData(object = seurat_object)
#'
#' # Analyze with Seurat
#' VlnPlot(seurat_object, features=c("VIM", "ZEB1", "CDH1"))
#' # Run MAGIC and reset the active assay
#' seurat_object <- magic(seurat_object)
#' seurat_object@active.assay <- "MAGIC_RNA"
#'
#' # Analyze with Seurat
#' VlnPlot(seurat_object, features = c("VIM", "ZEB1", "CDH1"))
#' }
#'
#' @export
#'
magic <- function(data, ...) {
UseMethod(generic = 'magic', object = data)
UseMethod(generic = "magic", object = data)
}

#' @rdname magic
#' @export
#'
magic.default <- function(
data,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = 'exact',
init = NULL,
t.max = 20,
knn.dist.method = 'euclidean',
verbose = 1,
n.jobs = 1,
seed = NULL,
# deprecated args
k=NULL, alpha=NULL,
...
) {
data,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = "exact",
init = NULL,
t.max = 20,
knn.dist.method = "euclidean",
verbose = 1,
n.jobs = 1,
seed = NULL,
# deprecated args
k = NULL, alpha = NULL,
...) {
# check installation
if (!reticulate::py_module_available(module = "magic") || (is.null(pymagic))) load_pymagic()
# check for deprecated arguments
Expand All @@ -149,7 +143,7 @@ magic.default <- function(
seed <- check.int.or.null(seed)
verbose <- check.int.or.null(verbose)
decay <- check.double.or.null(decay)
t <- check.int.or.string(t, 'auto')
t <- check.int.or.string(t, "auto")
if (!methods::is(object = data, "Matrix")) {
data <- as.matrix(x = data)
}
Expand Down Expand Up @@ -228,11 +222,11 @@ magic.default <- function(
colnames(x = result) <- gene_names
rownames(x = result) <- rownames(data)
result <- as.data.frame(x = result)
result <- list(
"result" = result,
"operator" = operator,
"params" = params
)
result <- list(
"result" = result,
"operator" = operator,
"params" = params
)
class(x = result) <- c("magic", "list")
return(result)
}
Expand All @@ -242,22 +236,21 @@ magic.default <- function(
#' @method magic seurat
#'
magic.seurat <- function(
data,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = "exact",
init = NULL,
t.max = 20,
knn.dist.method = 'euclidean',
verbose = 1,
n.jobs = 1,
seed = NULL,
...
) {
data,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = "exact",
init = NULL,
t.max = 20,
knn.dist.method = "euclidean",
verbose = 1,
n.jobs = 1,
seed = NULL,
...) {
if (requireNamespace("Seurat", quietly = TRUE)) {
results <- magic(
data = as.matrix(x = t(x = data@data)),
Expand Down Expand Up @@ -307,29 +300,28 @@ magic.seurat <- function(
#' @method magic Seurat
#'
magic.Seurat <- function(
data,
assay = NULL,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = 'exact',
init = NULL,
t.max = 20,
knn.dist.method = 'euclidean',
verbose = 1,
n.jobs = 1,
seed = NULL,
...
) {
data,
assay = NULL,
genes = NULL,
knn = 5,
knn.max = NULL,
decay = 1,
t = 3,
npca = 100,
solver = "exact",
init = NULL,
t.max = 20,
knn.dist.method = "euclidean",
verbose = 1,
n.jobs = 1,
seed = NULL,
...) {
if (requireNamespace("Seurat", quietly = TRUE)) {
if (is.null(x = assay)) {
assay <- Seurat::DefaultAssay(object = data)
}
results <- magic(
data = t(x = Seurat::GetAssayData(object = data, slot = 'data', assay = assay)),
data = t(x = Seurat::GetAssayData(object = data, slot = "data", assay = assay)),
genes = genes,
knn = knn,
knn.max = knn.max,
Expand All @@ -345,11 +337,13 @@ magic.Seurat <- function(
seed = seed,
...
)
assay_name <- paste0('MAGIC_', assay)
assay_name <- paste0("MAGIC_", assay)
data[[assay_name]] <- Seurat::CreateAssayObject(data = t(x = as.matrix(x = results$result)))
print(paste0("Added MAGIC output to ", assay_name, ". To use it, pass assay='", assay_name,
"' to downstream methods or set DefaultAssay(seurat_object) <- '", assay_name, "'."))
Seurat::Tool(object = data) <- results[c('operator', 'params')]
print(paste0(
"Added MAGIC output to ", assay_name, ". To use it, pass assay='", assay_name,
"' to downstream methods or set DefaultAssay(seurat_object) <- '", assay_name, "'."
))
Seurat::Tool(object = data) <- results[c("operator", "params")]
return(data)
} else {
message("Seurat package not available. Running default MAGIC implementation.")
Expand Down Expand Up @@ -380,26 +374,26 @@ magic.Seurat <- function(
#' @param ... Arguments for print()
#' @examples
#' if (pymagic_is_available()) {
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata)
#' print(data_magic)
#' ## MAGIC with elements
#' ## $result : (500, 197)
#' ## $operator : Python MAGIC operator
#' ## $params : list with elements (data, knn, decay, t, npca, knn.dist.method)
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata)
#' print(data_magic)
#' ## MAGIC with elements
#' ## $result : (500, 197)
#' ## $operator : Python MAGIC operator
#' ## $params : list with elements (data, knn, decay, t, npca, knn.dist.method)
#' }
#' @rdname print
#' @method print magic
#' @export
print.magic <- function(x, ...) {
result <- paste0("MAGIC with elements\n",
" $result : (", nrow(x$result), ", ",
ncol(x$result), ")\n",
" $operator : Python MAGIC operator\n",
" $params : list with elements (",
paste(names(x$params), collapse = ", "), ")")
result <- paste0(
"MAGIC with elements\n",
" $result : (", nrow(x$result), ", ",
ncol(x$result), ")\n",
" $operator : Python MAGIC operator\n",
" $params : list with elements (",
paste(names(x$params), collapse = ", "), ")"
)
cat(result)
}

Expand All @@ -409,18 +403,16 @@ print.magic <- function(x, ...) {
#' @param ... Arguments for summary()
#' @examples
#' if (pymagic_is_available()) {
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata)
#' summary(data_magic)
#' ## ZEB1
#' ## Min. :0.01071
#' ## 1st Qu.:0.01119
#' ## Median :0.01130
#' ## Mean :0.01129
#' ## 3rd Qu.:0.01140
#' ## Max. :0.01201
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata)
#' summary(data_magic)
#' ## ZEB1
#' ## Min. :0.01071
#' ## 1st Qu.:0.01119
#' ## Median :0.01130
#' ## Mean :0.01129
#' ## 3rd Qu.:0.01140
#' ## Max. :0.01201
#' }
#' @rdname summary
#' @method summary magic
Expand Down Expand Up @@ -463,12 +455,10 @@ as.data.frame.magic <- function(x, ...) {
#' @param ... Arguments for ggplot()
#' @examples
#' if (pymagic_is_available() && require(ggplot2)) {
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))
#' ggplot(data_magic, aes(VIM, CDH1, colour=ZEB1)) +
#' geom_point()
#'
#' data(magic_testdata)
#' data_magic <- magic(magic_testdata, genes = c("VIM", "CDH1", "ZEB1"))
#' ggplot(data_magic, aes(VIM, CDH1, colour = ZEB1)) +
#' geom_point()
#' }
#' @rdname ggplot
#' @method ggplot magic
Expand Down
2 changes: 1 addition & 1 deletion Rmagic/R/preprocessing.R
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
#' @import Matrix
#'
#' @export
library.size.normalize <- function(data, verbose=FALSE) {
library.size.normalize <- function(data, verbose = FALSE) {
if (verbose) {
message(paste0(
"Normalizing library sizes for ",
Expand Down

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