[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot] · pre-commit-ci[bot] · commit 2427dd96a0bb · 2025-11-03T17:13:49.000Z
for more information, see https://pre-commit.ci
diff --git a/R/DOT.R b/R/DOT.R
@@ -6,7 +6,6 @@ build_model_dot <- function() {
 }
 
 
-
 #' Deconvolute DOT
 #'
 #' @param single_cell_obj Single Cell Experiment
diff --git a/R/benchmarking.R b/R/benchmarking.R
@@ -121,9 +121,6 @@ plot_scatter <- function(spe = NULL, value1, value2, spe1 = NULL, spe2 = NULL, l
 }
 
 
-
-
-
 #' Compare Signatures
 #'
 #' @param signature1 signature
diff --git a/R/cluster.R b/R/cluster.R
@@ -66,7 +66,6 @@ cluster <- function(spe,
     cli::cli_alert_info(paste("Cluster resolution:", toString(clusres)))
 
 
-
     cli::cli_progress_step("Extracting data", msg_done = "Extracted data for clustering")
 
     # create seurat object
@@ -146,7 +145,6 @@ cluster <- function(spe,
   }
 
 
-
   cli::cli_progress_done()
 
   return(spe)
@@ -200,7 +198,6 @@ get_cluster_features <- function(spe,
   clusters <- colData(spe)[, clusterid]
 
 
-
   # Scores
   if (spmethod == "expression") {
     if (is.element("cpm", assayNames(spe)) && !is.null(spe@assays@data$cpm)) {
diff --git a/R/deconvolution_algorithms.R b/R/deconvolution_algorithms.R
@@ -285,8 +285,6 @@ deconvolute <- function(spatial_obj, signature = NULL, single_cell_obj = NULL,
   cli::cli_progress_step("testing parameter", msg_done = "parameter OK")
 
 
-
-
   if (is.null(spatial_obj)) {
     stop("Parameter 'spatial_obj' is missing or null, but is required.")
   }
diff --git a/R/preprocess.R b/R/preprocess.R
@@ -106,7 +106,6 @@ preprocess <- function(object, min_umi = 500, max_umi = NULL, assay = "counts",
   }
 
 
-
   cli::cli_progress_step(
     msg = "Checking for ENSEMBL Identifiers",
     msg_done = "Finished Preprocessing"
diff --git a/R/spatial_correlation.R b/R/spatial_correlation.R
@@ -96,7 +96,6 @@ spatialcorr <- function(spe,
   }
 
 
-
   # Select variables of interests
   # If variables is not provided but method is specified, the function selects variables based on those available in the dataset that start with the specified method.
   if (is.null(variables) && !is.null(method)) {
diff --git a/R/subset.R b/R/subset.R
@@ -124,10 +124,6 @@ subsetSCE <- function(sce, cell_type_col = "celltype_major", scenario = "even",
 }
 
 
-
-
-
-
 #' Isolate Regions within a SpatialExperiment Object
 #'
 #' Tailor a `SpatialExperiment` object to focus on specific areas by defining ranges in the spatial coordinates.
diff --git a/R/utils.R b/R/utils.R
@@ -305,7 +305,6 @@ checkENSEMBL <- function(names) {
 }
 
 
-
 #' Annotate Specific Spots within a SpatialExperiment Object
 #'
 #' This function allows for the annotation of specified spots within a `SpatialExperiment` object.
diff --git a/R/visualization.R b/R/visualization.R
@@ -479,7 +479,6 @@ plot_comparison <- function(spe, cell_type_1 = NULL, cell_type_2 = NULL,
 }
 
 
-
 #' Function to plot gene expression
 #'
 #' Generate Hex Plot of a SpatialExperiment containing deconvolution results
@@ -728,8 +727,6 @@ make_baseplot <- function(spe, df, to_plot, palette = "Mako", transform_scale =
   }
 
 
-
-
   # Check if plot is smoothed
   if (smooth) {
     smooth_suffix <- "smoothed"
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
@@ -11,7 +11,6 @@ test_that("convert human to mouse with valid gene symbols", {
 })
 
 
-
 ad <- spe_to_ad(spe, assay = "counts")
 
 test_that("spe_to_ad returns an AnnData object", {
diff --git a/tests/testthat/test-signature.R b/tests/testthat/test-signature.R
@@ -21,7 +21,6 @@ test_that("Immunedeconv models works", {
 })
 
 
-
 # Test for input validation in build_model
 test_that("build_model requires non-null single_cell_obj", {
   expect_error(build_model(NULL, method = "rctd"), "Parameter 'single_cell_obj' missing or null, but is required")
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -14,7 +14,6 @@ testthat::test_that("subsetSCE subsets the SingleCellExperiment correctly", {
 })
 
 
-
 testthat::test_that("Normalization works", {
   normalized <- spacedeconv::normalize(sce, method = "cpm", assay = "counts")
 
diff --git a/tests/testthat/test-visualization.R b/tests/testthat/test-visualization.R
@@ -23,8 +23,6 @@ test_that("Plot Umi Count works", {
 })
 
 
-
-
 test_that("Plot_post_abundant works", {
   p <- plot_most_abundant(spe, method = "estimate")
 

Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,6 @@ build_model_dot <- function() {`
`6`	`6`	`}`
`7`	`7`
`8`	`8`
`9`		`-`
`10`	`9`	`#' Deconvolute DOT`
`11`	`10`	`#'`
`12`	`11`	`#' @param single_cell_obj Single Cell Experiment`
Original file line number	Diff line number	Diff line change
`@@ -121,9 +121,6 @@ plot_scatter <- function(spe = NULL, value1, value2, spe1 = NULL, spe2 = NULL, l`
`121`	`121`	`}`
`122`	`122`
`123`	`123`
`124`		`-`
`125`		`-`
`126`		`-`
`127`	`124`	`#' Compare Signatures`
`128`	`125`	`#'`
`129`	`126`	`#' @param signature1 signature`
Original file line number	Diff line number	Diff line change
`@@ -285,8 +285,6 @@ deconvolute <- function(spatial_obj, signature = NULL, single_cell_obj = NULL,`
`285`	`285`	`cli::cli_progress_step("testing parameter", msg_done = "parameter OK")`
`286`	`286`
`287`	`287`
`288`		`-`
`289`		`-`
`290`	`288`	`if (is.null(spatial_obj)) {`
`291`	`289`	`stop("Parameter 'spatial_obj' is missing or null, but is required.")`
`292`	`290`	`}`
Original file line number	Diff line number	Diff line change
`@@ -106,7 +106,6 @@ preprocess <- function(object, min_umi = 500, max_umi = NULL, assay = "counts",`
`106`	`106`	`}`
`107`	`107`
`108`	`108`
`109`		`-`
`110`	`109`	`cli::cli_progress_step(`
`111`	`110`	`msg = "Checking for ENSEMBL Identifiers",`
`112`	`111`	`msg_done = "Finished Preprocessing"`
Original file line number	Diff line number	Diff line change
`@@ -96,7 +96,6 @@ spatialcorr <- function(spe,`
`96`	`96`	`}`
`97`	`97`
`98`	`98`
`99`		`-`
`100`	`99`	`# Select variables of interests`
`101`	`100`	`# If variables is not provided but method is specified, the function selects variables based on those available in the dataset that start with the specified method.`
`102`	`101`	`if (is.null(variables) && !is.null(method)) {`
Original file line number	Diff line number	Diff line change
`@@ -124,10 +124,6 @@ subsetSCE <- function(sce, cell_type_col = "celltype_major", scenario = "even",`
`124`	`124`	`}`
`125`	`125`
`126`	`126`
`127`		`-`
`128`		`-`
`129`		`-`
`130`		`-`
`131`	`127`	`#' Isolate Regions within a SpatialExperiment Object`
`132`	`128`	`#'`
`133`	`129`	#' Tailor a `SpatialExperiment` object to focus on specific areas by defining ranges in the spatial coordinates.
Original file line number	Diff line number	Diff line change
`@@ -305,7 +305,6 @@ checkENSEMBL <- function(names) {`
`305`	`305`	`}`
`306`	`306`
`307`	`307`
`308`		`-`
`309`	`308`	`#' Annotate Specific Spots within a SpatialExperiment Object`
`310`	`309`	`#'`
`311`	`310`	#' This function allows for the annotation of specified spots within a `SpatialExperiment` object.
Original file line number	Diff line number	Diff line change
`@@ -479,7 +479,6 @@ plot_comparison <- function(spe, cell_type_1 = NULL, cell_type_2 = NULL,`
`479`	`479`	`}`
`480`	`480`
`481`	`481`
`482`		`-`
`483`	`482`	`#' Function to plot gene expression`
`484`	`483`	`#'`
`485`	`484`	`#' Generate Hex Plot of a SpatialExperiment containing deconvolution results`
`@@ -728,8 +727,6 @@ make_baseplot <- function(spe, df, to_plot, palette = "Mako", transform_scale =`
`728`	`727`	`}`
`729`	`728`
`730`	`729`
`731`		`-`
`732`		`-`
`733`	`730`	`# Check if plot is smoothed`
`734`	`731`	`if (smooth) {`
`735`	`732`	`smooth_suffix <- "smoothed"`