This argument should always be present for specific methods of `spatialPatterns()` and `modelSearch()`
Milan Malfait authored on 01/06/2021 10:59:37
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@@ -91,12 +91,13 @@ NULL |
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) |
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} |
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-#' |
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#' @import methods |
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#' @export |
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#' @rdname spatialPatterns |
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-setGeneric("spatialPatterns", function(x, ...)
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- standardGeneric("spatialPatterns"))
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+setGeneric("spatialPatterns",
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+ function(x, de_results, ...) standardGeneric("spatialPatterns"),
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+ signature = "x" |
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+) |
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#' @export |
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#' @rdname spatialPatterns |
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@@ -104,7 +105,7 @@ setGeneric("spatialPatterns", function(x, ...)
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#' @importFrom SpatialExperiment spatialCoords spatialCoordsNames<- |
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#' @importFrom checkmate assert_data_frame assert_number assert_int assert_flag |
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setMethod("spatialPatterns", "SpatialExperiment",
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- function(x, assay_type = "counts", de_results, qval_thresh = 0.05, |
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+ function(x, de_results, assay_type = "counts", qval_thresh = 0.05, |
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n_patterns, length, verbose = FALSE) {
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assert_data_frame(de_results, all.missing = FALSE) |
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assert_number(qval_thresh, null.ok = TRUE) |
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@@ -79,7 +79,10 @@ NULL |
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#' @import methods |
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#' @export |
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#' @rdname modelSearch |
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-setGeneric("modelSearch", function(x, ...) standardGeneric("modelSearch"))
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+setGeneric("modelSearch",
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+ function(x, de_results, ...) standardGeneric("modelSearch"),
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+ signature = "x" |
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+) |
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#' @export |
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#' @rdname modelSearch |
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@@ -87,7 +90,7 @@ setGeneric("modelSearch", function(x, ...) standardGeneric("modelSearch"))
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#' @importFrom SpatialExperiment spatialCoords spatialCoordsNames<- |
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#' @importFrom checkmate assert_data_frame assert_number assert_flag |
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setMethod("modelSearch", "SpatialExperiment",
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- function(x, assay_type = "counts", de_results, qval_thresh=0.05, |
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+ function(x, de_results, assay_type = "counts", qval_thresh=0.05, |
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verbose = FALSE) {
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assert_data_frame(de_results, all.missing = FALSE) |
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assert_number(qval_thresh, null.ok = TRUE) |
| ... | ... |
@@ -5,12 +5,12 @@ |
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\alias{modelSearch,SpatialExperiment-method}
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\title{Classify Spatially Variable Genes to interpretable fitting classes}
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\usage{
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-modelSearch(x, ...) |
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+modelSearch(x, de_results, ...) |
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\S4method{modelSearch}{SpatialExperiment}(
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x, |
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- assay_type = "counts", |
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de_results, |
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+ assay_type = "counts", |
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qval_thresh = 0.05, |
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verbose = FALSE |
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) |
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@@ -18,13 +18,13 @@ modelSearch(x, ...) |
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\arguments{
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\item{x}{\linkS4class{SpatialExperiment} object.}
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+\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.}
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+ |
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\item{...}{For the generic, arguments to pass to specific methods.}
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\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use
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as input. Defaults to \code{"counts"}.}
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-\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.}
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- |
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\item{qval_thresh}{\code{numeric} scalar, specifying the q-value significance
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threshold to filter \code{de_results}. Only rows in \code{de_results} with
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\code{qval < qval_thresh} will be kept. To disable, set \code{qval_thresh = NULL}.}
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@@ -5,12 +5,12 @@ |
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\alias{spatialPatterns,SpatialExperiment-method}
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\title{Automatic expression histology in \strong{SpatialDE}}
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\usage{
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-spatialPatterns(x, ...) |
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+spatialPatterns(x, de_results, ...) |
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\S4method{spatialPatterns}{SpatialExperiment}(
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x, |
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- assay_type = "counts", |
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de_results, |
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+ assay_type = "counts", |
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qval_thresh = 0.05, |
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n_patterns, |
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length, |
| ... | ... |
@@ -20,13 +20,13 @@ spatialPatterns(x, ...) |
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\arguments{
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\item{x}{\linkS4class{SpatialExperiment} object.}
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+\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.}
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+ |
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\item{...}{For the generic, arguments to pass to specific methods.}
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| 24 | 26 |
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\item{assay_type}{A \code{character} string specifying the assay from \code{x} to use
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as input. Defaults to \code{"counts"}.}
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| 27 | 29 |
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-\item{de_results}{\code{data.frame} resulting from \code{\link[=run]{run()}} or \code{\link[=spatialDE]{spatialDE()}}.}
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- |
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\item{qval_thresh}{\code{numeric} scalar, specifying the q-value significance
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threshold to filter \code{de_results}. Only rows in \code{de_results} with
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| 32 | 32 |
\code{qval < qval_thresh} will be kept. To disable, set \code{qval_thresh = NULL}.}
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