run biocstyle

jiajic · Nov 16, 2024 · 2a83ded · 2a83ded
1 parent 86bd01f
commit 2a83ded
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Showing 45 changed files with 2,848 additions and 2,584 deletions.
diff --git a/R/NN_network.R b/R/NN_network.R
@@ -128,22 +128,21 @@ NULL
 
 #' @rdname createNetwork
 #' @export
-createNetwork <- function(
-        x,
-        type = c("sNN", "kNN", "delaunay"),
-        method = c("dbscan", "geometry", "RTriangle", "deldir"),
-        node_ids = NULL,
-        include_distance = TRUE,
-        include_weight = TRUE,
-        as.igraph = TRUE,
-        verbose = NULL,
-        ...) {
+createNetwork <- function(x,
+    type = c("sNN", "kNN", "delaunay"),
+    method = c("dbscan", "geometry", "RTriangle", "deldir"),
+    node_ids = NULL,
+    include_distance = TRUE,
+    include_weight = TRUE,
+    as.igraph = TRUE,
+    verbose = NULL,
+    ...) {
     # NSE vars
     from <- to <- NULL
 
     # check params
     type <- match.arg(type, choices = c("sNN", "kNN", "delaunay"))
-    
+
     mdef <- c("dbscan", "geometry", "RTriangle", "deldir")
     if (type %in% c("sNN", "kNN")) {
         mchoices <- c("dbscan")
@@ -153,7 +152,7 @@ createNetwork <- function(
         mchoices <- c("geometry", "RTriangle", "deldir")
         if (identical(method, mdef)) method <- mchoices
     }
-    
+
     method <- switch(type,
         "sNN" = match.arg(method, choices = mchoices, several.ok = TRUE),
         "kNN" = match.arg(method, choices = mchoices, several.ok = TRUE),
@@ -162,9 +161,11 @@ createNetwork <- function(
             match.arg(method, choices = mchoices, several.ok = TRUE)
         }
     )
-
-    vmsg(.is_debug = TRUE, sprintf("network\n type: %s\n method: %s",
-                                   type, method))
+
+    vmsg(.is_debug = TRUE, sprintf(
+        "network\n type: %s\n method: %s",
+        type, method
+    ))
 
     # get common params
     alist <- list(
@@ -225,12 +226,11 @@ createNetwork <- function(
 
 
 # x input is a matrix
-.net_dt_knn <- function(
-        x, k = 30L, include_weight = TRUE, include_distance = TRUE,
-        filter = FALSE,
-        maximum_distance = NULL, minimum_k = 0L,
-        weight_fun = function(d) 1 / (1 + d),
-        verbose = NULL, ...) {
+.net_dt_knn <- function(x, k = 30L, include_weight = TRUE, include_distance = TRUE,
+    filter = FALSE,
+    maximum_distance = NULL, minimum_k = 0L,
+    weight_fun = function(d) 1 / (1 + d),
+    verbose = NULL, ...) {
     # NSE vars
     from <- to <- distance <- NULL
 
@@ -283,11 +283,10 @@ createNetwork <- function(
 }
 
 # x input is a matrix
-.net_dt_snn <- function(
-        x, k = 30L, include_weight = TRUE, include_distance = TRUE,
-        top_shared = 3L, minimum_shared = 5L,
-        weight_fun = function(d) 1 / (1 + d),
-        verbose = NULL, ...) {
+.net_dt_snn <- function(x, k = 30L, include_weight = TRUE, include_distance = TRUE,
+    top_shared = 3L, minimum_shared = 5L,
+    weight_fun = function(d) 1 / (1 + d),
+    verbose = NULL, ...) {
     # NSE vars
     from <- to <- shared <- distance <- NULL
 
@@ -334,10 +333,9 @@ createNetwork <- function(
     return(snn_network_dt)
 }
 
-.net_dt_del_geometry <- function(
-        x, include_weight = TRUE, options = "Pp", maximum_distance = "auto",
-        minimum_k = 0L, weight_fun = function(d) 1 / d,
-        ...) {
+.net_dt_del_geometry <- function(x, include_weight = TRUE, options = "Pp", maximum_distance = "auto",
+    minimum_k = 0L, weight_fun = function(d) 1 / d,
+    ...) {
     package_check("geometry", repository = "CRAN:geometry")
 
     # data.table variables
@@ -388,10 +386,9 @@ createNetwork <- function(
     return(out_object)
 }
 
-.net_dt_del_rtriangle <- function(
-        x, include_weight = TRUE, maximum_distance = "auto", minimum_k = 0L,
-        Y = TRUE, j = TRUE, S = 0, weight_fun = function(d) 1 / d,
-        ...) {
+.net_dt_del_rtriangle <- function(x, include_weight = TRUE, maximum_distance = "auto", minimum_k = 0L,
+    Y = TRUE, j = TRUE, S = 0, weight_fun = function(d) 1 / d,
+    ...) {
     # NSE vars
     from <- to <- distance <- NULL
 
@@ -433,10 +430,9 @@ createNetwork <- function(
     return(out_object)
 }
 
-.net_dt_del_deldir <- function(
-        x, include_weight = TRUE, maximum_distance = "auto", minimum_k = 0L,
-        weight_fun = function(d) 1 / d,
-        ...) {
+.net_dt_del_deldir <- function(x, include_weight = TRUE, maximum_distance = "auto", minimum_k = 0L,
+    weight_fun = function(d) 1 / d,
+    ...) {
     # NSE variables
     from <- to <- distance <- NULL
 
@@ -625,23 +621,22 @@ edge_distances <- function(x, y, x_node_ids = NULL) {
 #'
 #' createNearestNetwork(g)
 #' @export
-createNearestNetwork <- function(
-        gobject,
-        spat_unit = NULL,
-        feat_type = NULL,
-        type = c("sNN", "kNN"),
-        dim_reduction_to_use = "pca",
-        dim_reduction_name = NULL,
-        dimensions_to_use = seq_len(10),
-        feats_to_use = NULL,
-        expression_values = c("normalized", "scaled", "custom"),
-        name = NULL,
-        return_gobject = TRUE,
-        k = 30,
-        minimum_shared = 5,
-        top_shared = 3,
-        verbose = TRUE,
-        ...) {
+createNearestNetwork <- function(gobject,
+    spat_unit = NULL,
+    feat_type = NULL,
+    type = c("sNN", "kNN"),
+    dim_reduction_to_use = "pca",
+    dim_reduction_name = NULL,
+    dimensions_to_use = seq_len(10),
+    feats_to_use = NULL,
+    expression_values = c("normalized", "scaled", "custom"),
+    name = NULL,
+    return_gobject = TRUE,
+    k = 30,
+    minimum_shared = 5,
+    top_shared = 3,
+    verbose = TRUE,
+    ...) {
     # Set feat_type and spat_unit
     spat_unit <- set_default_spat_unit(
         gobject = gobject,
@@ -882,15 +877,16 @@ createNearestNetwork <- function(
 #'
 #' addNetworkLayout(g)
 #' @export
-addNetworkLayout <- function(gobject,
-    spat_unit = NULL,
-    feat_type = NULL,
-    nn_network_to_use = "sNN",
-    network_name = "sNN.pca",
-    layout_type = c("drl"),
-    options_list = NULL,
-    layout_name = "layout",
-    return_gobject = TRUE) {
+addNetworkLayout <- function(
+        gobject,
+        spat_unit = NULL,
+        feat_type = NULL,
+        nn_network_to_use = "sNN",
+        network_name = "sNN.pca",
+        layout_type = c("drl"),
+        options_list = NULL,
+        layout_name = "layout",
+        return_gobject = TRUE) {
     ## checks
     if (is.null(nn_network_to_use) | is.null(network_name)) {
         stop("\n first create a nearest network \n")