consistent format

TrigosTeam · Apr 26, 2022 · 3afc583 · 3afc583
1 parent dfd6fa4
commit 3afc583
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Showing 16 changed files with 85 additions and 60 deletions.
diff --git a/R/multiple_background_images.R b/R/multiple_background_images.R
@@ -42,7 +42,7 @@ multiple_background_images <- function(bg_sample = bg1,
                                        idents = c("Tumour", "Immune","Others"),
                                        props = list(rep(0.1, 9),
                                                     seq(0, 0.4, 0.05),
-                                                    seq(0.9,0.5,-0.05)),
+                                                    seq(0.9, 0.5, -0.05)),
                                        plot_image = TRUE,
                                        plot_colours = NULL){
     ## CHECK

diff --git a/R/multiple_images_with_clusters.R b/R/multiple_images_with_clusters.R
@@ -52,10 +52,9 @@
 #' @export
 #' @examples
 #' set.seed(610)
-#' cluster_image_list <- multiple_images_with_clusters(bg_sample = bg1,
-#' cluster_shape=2, prop_infiltration = c(0.1, 0.3), cluster_size = c(300,600),
+#' cluster_image_list <- multiple_images_with_clusters(bg_sample=bg1,
+#' cluster_shape=2, prop_infiltration=0.1, cluster_size = seq(200,1000,100),
 #' cluster_loc_x = 0, cluster_loc_y = 0, plot_image = TRUE)
-
 multiple_images_with_clusters <- function(bg_sample = bg1,
                                           cluster_shape = 2,
                                           prop_infiltration = 0.1,

diff --git a/R/multiple_images_with_immune_rings.R b/R/multiple_images_with_immune_rings.R
@@ -58,9 +58,8 @@
 #' set.seed(610)
 #' ring_image_list <- multiple_images_with_immune_rings(bg_sample = bg1,
 #' ring_shape = 1, prop_infiltration = 0, ring_width = seq(50,100,10),
-#' cluster_size = 300, cluster_loc_x = 0, cluster_loc_y = 0,
+#' cluster_size = 200, cluster_loc_x = 0, cluster_loc_y = 0,
 #' prop_ring_infiltration = seq(0, 0.2,0.05), plot_image = TRUE)
-
 multiple_images_with_immune_rings <- function(bg_sample = bg1,
                                               cluster_size = 200,
                                               ring_shape = 1,

diff --git a/R/simulate_clusters.R b/R/simulate_clusters.R
@@ -39,11 +39,12 @@
 #' @examples
 #' set.seed(610)
 #' cluster_image <- simulate_clusters(bg_sample = bg1,
-#' n_clusters = 1, cluster_properties= list(C1 = list(
-#' name_of_cluster_cell = "Tumour", size = 300, shape = "Oval", centre_loc =
-#' data.frame("x" = 500, "y" = 500), infiltration_types = c("Immune1", "Others"),
-#' infiltration_proportions = c(0.1, 0.05))))
-
+#' n_clusters=2, cluster_properties=list(C1=list(name_of_cluster_cell="Tumour",
+#' size=300, shape="Oval", centre_loc=data.frame("x"=500, "y"=500),
+#' infiltration_types=c("Immune1", "Others"), infiltration_proportions=c(0.1, 0.05)),
+#' C2=list(name_of_cluster_cell="Immune1", size=500, shape="Irregular",
+#' centre_loc=data.frame("x"=1500,"y"=500), infiltration_types=c("Immune2", "Others"),
+#' infiltration_proportions=c(0.1, 0.05))))
 simulate_clusters <- function(bg_sample = bg1,
                               n_clusters = 2,
                               bg_type = "Others",
@@ -68,7 +69,6 @@ simulate_clusters <- function(bg_sample = bg1,
                               plot_categories = NULL,
                               plot_colours = NULL
 ){
-
     ## CHECK
     if (!is.data.frame(bg_sample) & !methods::is(bg_sample, "SingleCellExperiment")) {
         stop("`bg_sample` should be either a data.frame or a SingleCellExperiment object!")

diff --git a/R/simulate_double_rings.R b/R/simulate_double_rings.R
@@ -65,7 +65,7 @@ simulate_double_rings <- function(bg_sample = bg1,
                                   n_dr = 2,
                                   win = NULL,
                                   dr_properties = list(
-                                      I1 = list(
+                                      D1 = list(
                                           name_of_cluster_cell = "Tumour",
                                           size = 300,
                                           shape = "Circle",
@@ -81,7 +81,7 @@ simulate_double_rings <- function(bg_sample = bg1,
                                           double_ring_infiltration_types = c("Others"),
                                           double_ring_infiltration_proportions = c(0.15)
                                       ),
-                                      I2 = list(
+                                      D2 = list(
                                           name_of_cluster_cell = "Tumour",
                                           size = 300,
                                           shape = "Oval",

diff --git a/R/simulate_immune_rings.R b/R/simulate_immune_rings.R
@@ -41,14 +41,19 @@
 #' @examples
 #' set.seed(610)
 #' # manually define the properties of the immune ring
-#' ir_properties <- list(I1 = list(name_of_cluster_cell = "Tumour",
-#' size = 600,shape = "Circle",centre_loc = data.frame("x" = 930, "y" = 1000),
-#' infiltration_types = c("Immune1", "Immune2", "Others"), infiltration_proportions
-#' = c(0.15, 0.05, 0.05), name_of_ring_cell = "Immune1", immune_ring_width = 150,
-#' immune_ring_infiltration_types = c("Others"), immune_ring_infiltration_proportions = c(0.15)))
+#' ir_properties <- list(I1=list(name_of_cluster_cell="Tumour", size=600,
+#' shape="Circle",centre_loc=data.frame("x"=930, "y"=1000),
+#' infiltration_types=c("Immune1", "Immune2", "Others"), infiltration_proportions
+#'=c(0.15, 0.05, 0.05), name_of_ring_cell="Immune1", immune_ring_width=150,
+#' immune_ring_infiltration_types=c("Others"), immune_ring_infiltration_proportions=c(0.15)),
+#' I2=list(name_of_cluster_cell="Tumour", size=500, shape="Oval",
+#' centre_loc=data.frame("x"=1330, "y"=1100), infiltration_types=c("Immune1", "Immune2", "Others"),
+#' infiltration_proportions=c(0.15, 0.05, 0.05), name_of_ring_cell="Immune1",
+#' immune_ring_width=150, immune_ring_infiltration_types=c("Others"),
+#' immune_ring_infiltration_proportions=c(0.15)))
 #' # simulate immune rings (`n_ir` should match the length of `ir_properties`)
-#' immune_ring_image <- simulate_immune_rings(bg_sample = bg1,
-#' n_ir = 1, ir_properties = ir_properties)
+#' immune_ring_image <- simulate_immune_rings(bg_sample=bg1,
+#' n_ir=2, ir_properties=ir_properties)
 #'
 simulate_immune_rings <- function(bg_sample = bg1,
                                   bg_type = "Others",

diff --git a/R/simulate_mixing.R b/R/simulate_mixing.R
@@ -29,10 +29,9 @@
 #'
 #' @examples
 #' set.seed(610)
-#' mix_background <- simulate_mixing(bg_sample = bg1,
-#' idents = c("Tumour","Immune", "Others"), props = c(0.2, 0.4,  0.4))
-#'
-
+#' mix_background <- simulate_mixing(bg_sample=bg1,
+#' idents=c("Tumour","Immune", "Others"), props=c(0.2, 0.4,  0.4),
+#' plot_image=TRUE)
 simulate_mixing <- function(bg_sample = bg1,
                             idents = c("Tumour", "Immune", "Others"),
                             props = c(0.2, 0.4, 0.4),

diff --git a/man/TIS.Rd b/man/TIS.Rd
diff --git a/man/multiple_background_images.Rd b/man/multiple_background_images.Rd
diff --git a/man/multiple_images_with_clusters.Rd b/man/multiple_images_with_clusters.Rd
diff --git a/man/multiple_images_with_immune_rings.Rd b/man/multiple_images_with_immune_rings.Rd
diff --git a/man/simulate_clusters.Rd b/man/simulate_clusters.Rd
diff --git a/man/simulate_double_rings.Rd b/man/simulate_double_rings.Rd
diff --git a/man/simulate_immune_rings.Rd b/man/simulate_immune_rings.Rd
diff --git a/man/simulate_mixing.Rd b/man/simulate_mixing.Rd
diff --git a/man/simulate_stripes.Rd b/man/simulate_stripes.Rd