diff --git a/R/multiple_background_images.R b/R/multiple_background_images.R
index 511798e..1b58519 100644
--- 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
index 30ab9a9..bb2b261 100644
--- 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
index 1413e94..e927e94 100644
--- 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
index 4db5991..aafd707 100644
--- 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
index 5810911..e09ec8a 100644
--- 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
index 54fd46e..7ce897f 100644
--- 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
index f20dd84..c8393e9 100644
--- 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
index 6d423ad..82d9e55 100644
--- a/man/TIS.Rd
+++ b/man/TIS.Rd
@@ -85,10 +85,12 @@ stripes.}
 \item{plot_image}{Boolean. Whether the simulated image is plotted.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 An sce object of the simulated image
diff --git a/man/multiple_background_images.Rd b/man/multiple_background_images.Rd
index c56d4fd..728a6e3 100644
--- a/man/multiple_background_images.Rd
+++ b/man/multiple_background_images.Rd
@@ -31,7 +31,8 @@ number of images.}
 is TRUE.}
 
 \item{plot_colours}{String Vector. If plot_image is TRUE, this param is the
-corresponding colours for the \code{idents} arg.}
+corresponding colours for the \code{idents} arg. Default is NULL, the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A list of SCE objects
diff --git a/man/multiple_images_with_clusters.Rd b/man/multiple_images_with_clusters.Rd
index 3dd6ccb..f4afe34 100644
--- a/man/multiple_images_with_clusters.Rd
+++ b/man/multiple_images_with_clusters.Rd
@@ -55,10 +55,12 @@ The Y location of the cluster center offset.}
 TRUE.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A list of SCE objects
@@ -72,8 +74,8 @@ without the specification of any argument.
 }
 \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)
 }
 \seealso{
diff --git a/man/multiple_images_with_immune_rings.Rd b/man/multiple_images_with_immune_rings.Rd
index 977621b..333141f 100644
--- a/man/multiple_images_with_immune_rings.Rd
+++ b/man/multiple_images_with_immune_rings.Rd
@@ -64,10 +64,12 @@ infiltration in the region of immune rings.}
 TRUE.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-cateories to be plotted.}
+cateories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A list of sce objects
@@ -82,7 +84,7 @@ specification of any argument.
 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)
 }
 \seealso{
diff --git a/man/simulate_clusters.Rd b/man/simulate_clusters.Rd
index 18a26ce..2b475b5 100644
--- a/man/simulate_clusters.Rd
+++ b/man/simulate_clusters.Rd
@@ -44,10 +44,12 @@ for the format of this arg.}
 \item{plot_image}{Boolean. Whether the simulated image is plotted.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A data.frame of the simulated image
@@ -61,10 +63,12 @@ simulation of clusters without the specification of any argument.
 \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))))
 }
 \seealso{
 \code{\link{simulate_background_cells}} for all cell simulation,
diff --git a/man/simulate_double_rings.Rd b/man/simulate_double_rings.Rd
index 16b6dc7..039b00b 100644
--- a/man/simulate_double_rings.Rd
+++ b/man/simulate_double_rings.Rd
@@ -9,14 +9,14 @@ simulate_double_rings(
   bg_type = "Others",
   n_dr = 2,
   win = NULL,
-  dr_properties = list(I1 = list(name_of_cluster_cell = "Tumour", size = 300, shape =
+  dr_properties = list(D1 = list(name_of_cluster_cell = "Tumour", size = 300, shape =
     "Circle", centre_loc = data.frame(x = 1000, 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), name_of_double_ring_cell = "Immune2", double_ring_width = 100,
     double_ring_infiltration_types = c("Others"), double_ring_infiltration_proportions =
-    c(0.15)),      I2 = list(name_of_cluster_cell = "Tumour", size = 300, shape = "Oval",
+    c(0.15)),      D2 = list(name_of_cluster_cell = "Tumour", size = 300, shape = "Oval",
     centre_loc = data.frame(x = 1200, y = 1200), infiltration_types = c("Immune1",
     "Immune2", "Others"), infiltration_proportions = c(0.15, 0.05, 0.05),
     name_of_ring_cell = "Immune1", immune_ring_width = 150,
@@ -52,10 +52,12 @@ refer to the examples for the structure of \code{dr_properties}.}
 \item{plot_image}{Boolean. Whether the simulated image is plotted.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A data.frame of the simulated image
diff --git a/man/simulate_immune_rings.Rd b/man/simulate_immune_rings.Rd
index 90d6f60..e604129 100644
--- a/man/simulate_immune_rings.Rd
+++ b/man/simulate_immune_rings.Rd
@@ -48,10 +48,12 @@ the examples for the structure of \code{ir_properties}.}
 \item{plot_image}{Boolean. Whether the simulated image is plotted.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A data.frame of the simulated image
@@ -66,14 +68,19 @@ of immune rings without the specification of any argument.
 \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)
 
 }
 \seealso{
diff --git a/man/simulate_mixing.Rd b/man/simulate_mixing.Rd
index f0f388c..6b5921e 100644
--- a/man/simulate_mixing.Rd
+++ b/man/simulate_mixing.Rd
@@ -27,7 +27,8 @@ metadata of the SCE object should have colnames including
 \item{plot_image}{Boolean. Whether the simulated image is plotted.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{idents} arg.}
+correspond to the \code{idents} arg. Default is NULL - the predefined
+colour vector would be used for plotting..}
 }
 \value{
 A data.frame of the simulated image
@@ -41,9 +42,9 @@ argument.
 }
 \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)
 }
 \seealso{
 \code{\link{simulate_background_cells}} for all cell simulation,
diff --git a/man/simulate_stripes.Rd b/man/simulate_stripes.Rd
index fb49bf9..ba6cb65 100644
--- a/man/simulate_stripes.Rd
+++ b/man/simulate_stripes.Rd
@@ -40,10 +40,12 @@ structure of \code{stripe_properties}.}
 TRUE.}
 
 \item{plot_categories}{String Vector specifying the order of the cell
-categories to be plotted.}
+categories to be plotted. Default is NULL - the cell categories under the
+"Phenotype" column would be used for plotting.}
 
 \item{plot_colours}{String Vector specifying the order of the colours that
-correspond to the \code{plot_categories} arg.}
+correspond to the \code{plot_categories} arg. Default is NULL - the predefined
+colour vector would be used for plotting.}
 }
 \value{
 A data.frame of the simulated image