diff --git a/NAMESPACE b/NAMESPACE
index d2d7e38..04883e4 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,15 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(get_bottom_n_clonotypes)
 export(get_study)
-export(plot_reads_group_abundance)
-export(plot_clonal_prop_per_sample)
+export(get_top_n_clonotypes)
 export(plot_clonal_prop_per_group)
+export(plot_clonal_prop_per_sample)
 export(plot_clonotype_abundance)
-export(get_bottom_n_clonotypes)
-export(get_top_n_clonotypes)
 export(plot_diversity_index)
 export(plot_motif_counts)
+export(plot_reads_group_abundance)
 exportClasses(Basic)
 exportClasses(Clonality)
 exportClasses(Diversity)
diff --git a/R/plot_clonal_prop_per_group.R b/R/plot_clonal_prop_per_group.R
deleted file mode 100644
index 684ba83..0000000
--- a/R/plot_clonal_prop_per_group.R
+++ /dev/null
@@ -1,47 +0,0 @@
-#' Plot clonal proportion per group
-#'
-#' This function plots the clonal proportion per group.
-#'
-#' @param data A data frame of clonal proportion per group.
-#' @param attr_col Character. Attribute column name.
-#'
-#' @return A ggplot2 plot of clonal proportion per group.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
-#' clonal_prop <- proj@clonality@clonal_prop
-#' reTCR::plot_clonal_prop_per_group(clonal_prop, "cmv_status")
-#' }
-plot_clonal_prop_per_group <- function(data, attr_col) {
-  data[[attr_col]] <- as.factor(data[[attr_col]])
-  ggplot2::ggplot(
-    data,
-    ggplot2::aes_string(
-      x = attr_col,
-      y = "clonality_portion"
-    )
-  ) +
-    ggplot2::geom_violin(trim = FALSE, fill = "skyblue", alpha = 0.5) +
-    ggplot2::geom_boxplot(outlier.shape = NA, width = 0.1, alpha = 0.7) +
-    ggplot2::geom_jitter(width = 0, height = 0.1, size = 1.5, alpha = 0.6) +
-    ggplot2::theme_classic() +
-    ggplot2::labs(x = attr_col, y = "number of clonotypes") +
-    ggplot2::theme(
-      axis.text.x = ggplot2::element_text(
-        angle = 90, vjust = 0.5, hjust = 1, size = 10
-      ),
-      axis.text.y = ggplot2::element_text(
-        size = 12,
-        margin = ggplot2::margin(l = 10)
-      ),
-      axis.title.x = ggplot2::element_text(
-        size = 14,
-        margin = ggplot2::margin(t = 10)
-      ),
-      axis.title.y = ggplot2::element_text(size = 14),
-      legend.title = ggplot2::element_text(size = 14),
-      legend.text = ggplot2::element_text(size = 12)
-    )
-}
diff --git a/R/plot_clonal_prop_per_sample.R b/R/plot_clonal_prop_per_sample.R
deleted file mode 100644
index b37ba91..0000000
--- a/R/plot_clonal_prop_per_sample.R
+++ /dev/null
@@ -1,47 +0,0 @@
-#' Plot clonal proportion per sample
-#'
-#' This function plots the clonal proportion per sample.
-#'
-#' @param data A data frame of clonal proportion per sample.
-#' @param attr_col Character. Attribute column name.
-#'
-#' @return A ggplot2 plot of clonal proportion per sample.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
-#' clonal_prop <- proj@clonality@clonal_prop
-#' reTCR::plot_clonal_prop_per_sample(clonal_prop, "cmv_status")
-#' }
-plot_clonal_prop_per_sample <- function(data, attr_col) {
-  ggplot2::ggplot(
-    data,
-    ggplot2::aes(
-      x = sample,
-      y = clonality_portion,
-      fill = !!rlang::sym(attr_col)
-    )
-  ) +
-    ggplot2::geom_bar(stat = "identity", position = ggplot2::position_dodge()) +
-    ggplot2::labs(x = "sample", y = "number of clonotypes") +
-    ggplot2::theme_classic() +
-    ggplot2::theme(
-      axis.text.x = ggplot2::element_text(
-        angle = 90, vjust = 0.5, hjust = 1, size = 10
-      ),
-      axis.text.y = ggplot2::element_text(
-        size = 12,
-        margin = ggplot2::margin(l = 10)
-      ),
-      axis.title.x = ggplot2::element_text(
-        size = 14,
-        margin = ggplot2::margin(t = 10)
-      ),
-      axis.title.y = ggplot2::element_text(size = 14),
-      legend.title = ggplot2::element_text(size = 14),
-      legend.text = ggplot2::element_text(size = 12)
-    ) +
-    ggplot2::scale_y_continuous(expand = c(0, 0)) +
-    ggplot2::scale_fill_brewer(palette = "Set1", name = attr_col)
-}
diff --git a/R/plot_clonotype_abundance.R b/R/plot_clonotype_abundance.R
deleted file mode 100644
index e9801e9..0000000
--- a/R/plot_clonotype_abundance.R
+++ /dev/null
@@ -1,60 +0,0 @@
-#' Plot relative abundance for all clonotypes
-#'
-#' This function plots the relative abundance for all clonotypes.
-#'
-#' @param data A data frame of relative abundance for all clonotypes.
-#'
-#' @return A ggplot2 plot of relative abundance for all clonotypes.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
-#' reTCR::plot_clonotype_abundance(proj@clonality@abundance)
-#' }
-plot_clonotype_abundance <- function(data) {
-  label_order <- unique(data$clonotype_group)
-  colors <- RColorBrewer::brewer.pal(n = length(label_order), name = "Set1")
-
-  ggplot2::ggplot(
-    data,
-    ggplot2::aes(x = sample, y = relative_abundance, fill = clonotype_group)
-  ) +
-    ggplot2::geom_bar(
-      stat = "identity",
-      width = 0.5,
-      color = NA
-    ) +
-    ggplot2::scale_fill_manual(
-      values = colors,
-      breaks = label_order
-    ) +
-    ggplot2::labs(x = "sample", y = "clonotype frequency") +
-    ggplot2::theme_minimal() +
-    ggplot2::theme(
-      axis.text.x = ggplot2::element_text(
-        angle = 90,
-        vjust = 0.5,
-        hjust = 1,
-        size = 10
-      ),
-      axis.text.y = ggplot2::element_text(size = 10),
-      axis.title = ggplot2::element_text(size = 14),
-      legend.title = ggplot2::element_blank(),
-      legend.text = ggplot2::element_text(size = 12),
-      legend.position = "right",
-      panel.grid.major = ggplot2::element_blank(),
-      panel.grid.minor = ggplot2::element_blank(),
-      axis.line = ggplot2::element_line(color = "black"),
-      axis.text = ggplot2::element_text(margin = ggplot2::margin(t = 10)),
-      axis.ticks = ggplot2::element_line(color = "black", linewidth = 0.3),
-      strip.background = ggplot2::element_blank(),
-      strip.text = ggplot2::element_text(size = 12)
-    ) +
-    ggplot2::scale_x_discrete(
-      labels = function(x) {
-        stringr::str_wrap(x, width = 10)
-      }
-    ) +
-    ggplot2::scale_y_continuous(expand = c(0, 0))
-}
diff --git a/R/plot_reads_group_abundance.R b/R/plot_reads_group_abundance.R
deleted file mode 100644
index e5908ef..0000000
--- a/R/plot_reads_group_abundance.R
+++ /dev/null
@@ -1,62 +0,0 @@
-#' Plot reads group abundance for top 100 clonotypes
-#'
-#' This function plots reads group abundance for top 100 clonotypes.
-#'
-#' @param data A data frame of relative abundance for top 100 clonotypes.
-#'
-#' @return A ggplot2 plot of reads group abundance for top 100 clonotypes.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
-#' reTCR::plot_reads_group_abundance(proj@clonality@abundance_top)
-#' }
-plot_reads_group_abundance <- function(data) {
-  label_order <- unique(data$reads_group)
-  colors <- RColorBrewer::brewer.pal(n = length(label_order), name = "Set1")
-
-  df_counts <- data %>%
-    dplyr::filter(reads_group != "None") %>%
-    dplyr::group_by(sample, reads_group) %>%
-    dplyr::summarize(count = dplyr::n()) %>%
-    dplyr::ungroup()
-
-  ggplot2::ggplot(
-    df_counts,
-    ggplot2::aes(
-      x = sample,
-      y = count,
-      fill = reads_group
-    )
-  ) +
-    ggplot2::geom_bar(position = "stack", stat = "identity", width = 0.7) +
-    ggplot2::scale_fill_manual(
-      values = colors,
-      breaks = label_order,
-      name = "reads_group"
-    ) +
-    ggplot2::labs(x = "sample", y = "number of clonotypes") +
-    ggplot2::theme_minimal() +
-    ggplot2::theme(
-      axis.text.x = ggplot2::element_text(
-        angle = 90, vjust = 0.5, hjust = 1, size = 10
-      ),
-      axis.text.y = ggplot2::element_text(size = 10),
-      axis.title = ggplot2::element_text(size = 14),
-      legend.title = ggplot2::element_blank(),
-      legend.text = ggplot2::element_text(size = 12),
-      legend.position = "right",
-      panel.grid.major = ggplot2::element_blank(),
-      panel.grid.minor = ggplot2::element_blank(),
-      axis.line = ggplot2::element_line(color = "black"),
-      axis.text = ggplot2::element_text(margin = ggplot2::margin(t = 10)),
-      axis.ticks = ggplot2::element_line(color = "black", size = 0.3),
-      strip.background = ggplot2::element_blank(),
-      strip.text = ggplot2::element_text(size = 12)
-    ) +
-    ggplot2::scale_x_discrete(
-      labels = function(x) stringr::str_wrap(x, width = 10)
-    ) +
-    ggplot2::scale_y_continuous(expand = c(0, 0))
-}
diff --git a/R/utils-clonality-plot.R b/R/utils-clonality-plot.R
new file mode 100644
index 0000000..d79050e
--- /dev/null
+++ b/R/utils-clonality-plot.R
@@ -0,0 +1,219 @@
+#' Plot clonal proportion per sample
+#'
+#' This function plots the clonal proportion per sample.
+#'
+#' @param data A data frame of clonal proportion per sample.
+#' @param attr_col Character. Attribute column name.
+#'
+#' @return A ggplot2 plot of clonal proportion per sample.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
+#' clonal_prop <- proj@clonality@clonal_prop
+#' reTCR::plot_clonal_prop_per_sample(clonal_prop, "cmv_status")
+#' }
+plot_clonal_prop_per_sample <- function(data, attr_col) {
+  ggplot2::ggplot(
+    data,
+    ggplot2::aes(
+      x = sample,
+      y = clonality_portion,
+      fill = !!rlang::sym(attr_col)
+    )
+  ) +
+    ggplot2::geom_bar(stat = "identity", position = ggplot2::position_dodge()) +
+    ggplot2::labs(x = "sample", y = "number of clonotypes") +
+    ggplot2::theme_classic() +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90, vjust = 0.5, hjust = 1, size = 10
+      ),
+      axis.text.y = ggplot2::element_text(
+        size = 12,
+        margin = ggplot2::margin(l = 10)
+      ),
+      axis.title.x = ggplot2::element_text(
+        size = 14,
+        margin = ggplot2::margin(t = 10)
+      ),
+      axis.title.y = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_text(size = 14),
+      legend.text = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_y_continuous(expand = c(0, 0)) +
+    ggplot2::scale_fill_brewer(palette = "Set1", name = attr_col)
+}
+
+#' Plot clonal proportion per group
+#'
+#' This function plots the clonal proportion per group.
+#'
+#' @param data A data frame of clonal proportion per group.
+#' @param attr_col Character. Attribute column name.
+#'
+#' @return A ggplot2 plot of clonal proportion per group.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
+#' clonal_prop <- proj@clonality@clonal_prop
+#' reTCR::plot_clonal_prop_per_group(clonal_prop, "cmv_status")
+#' }
+plot_clonal_prop_per_group <- function(data, attr_col) {
+  data[[attr_col]] <- as.factor(data[[attr_col]])
+  ggplot2::ggplot(
+    data,
+    ggplot2::aes_string(
+      x = attr_col,
+      y = "clonality_portion"
+    )
+  ) +
+    ggplot2::geom_violin(trim = FALSE, fill = "skyblue", alpha = 0.5) +
+    ggplot2::geom_boxplot(outlier.shape = NA, width = 0.1, alpha = 0.7) +
+    ggplot2::geom_jitter(width = 0, height = 0.1, size = 1.5, alpha = 0.6) +
+    ggplot2::theme_classic() +
+    ggplot2::labs(x = attr_col, y = "number of clonotypes") +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90, vjust = 0.5, hjust = 1, size = 10
+      ),
+      axis.text.y = ggplot2::element_text(
+        size = 12,
+        margin = ggplot2::margin(l = 10)
+      ),
+      axis.title.x = ggplot2::element_text(
+        size = 14,
+        margin = ggplot2::margin(t = 10)
+      ),
+      axis.title.y = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_text(size = 14),
+      legend.text = ggplot2::element_text(size = 12)
+    )
+}
+
+#' Plot relative abundance for all clonotypes
+#'
+#' This function plots the relative abundance for all clonotypes.
+#'
+#' @param data A data frame of relative abundance for all clonotypes.
+#'
+#' @return A ggplot2 plot of relative abundance for all clonotypes.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status")
+#' reTCR::plot_clonotype_abundance(proj@clonality@abundance)
+#' }
+plot_clonotype_abundance <- function(data) {
+  label_order <- unique(data$clonotype_group)
+  colors <- RColorBrewer::brewer.pal(n = length(label_order), name = "Set1")
+
+  ggplot2::ggplot(
+    data,
+    ggplot2::aes(x = sample, y = relative_abundance, fill = clonotype_group)
+  ) +
+    ggplot2::geom_bar(
+      stat = "identity",
+      width = 0.5,
+      color = NA
+    ) +
+    ggplot2::scale_fill_manual(
+      values = colors,
+      breaks = label_order
+    ) +
+    ggplot2::labs(x = "sample", y = "clonotype frequency") +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90,
+        vjust = 0.5,
+        hjust = 1,
+        size = 10
+      ),
+      axis.text.y = ggplot2::element_text(size = 10),
+      axis.title = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_blank(),
+      legend.text = ggplot2::element_text(size = 12),
+      legend.position = "right",
+      panel.grid.major = ggplot2::element_blank(),
+      panel.grid.minor = ggplot2::element_blank(),
+      axis.line = ggplot2::element_line(color = "black"),
+      axis.text = ggplot2::element_text(margin = ggplot2::margin(t = 10)),
+      axis.ticks = ggplot2::element_line(color = "black", linewidth = 0.3),
+      strip.background = ggplot2::element_blank(),
+      strip.text = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_x_discrete(
+      labels = function(x) {
+        stringr::str_wrap(x, width = 10)
+      }
+    ) +
+    ggplot2::scale_y_continuous(expand = c(0, 0))
+}
+
+#' Plot reads group abundance for top 100 clonotypes
+#'
+#' This function plots reads group abundance for top 100 clonotypes.
+#'
+#' @param data A data frame of relative abundance for top 100 clonotypes.
+#'
+#' @return A ggplot2 plot of reads group abundance for top 100 clonotypes.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status")
+#' reTCR::plot_reads_group_abundance(proj@clonality@abundance_top)
+#' }
+plot_reads_group_abundance <- function(data) {
+  label_order <- unique(data$reads_group)
+  colors <- RColorBrewer::brewer.pal(n = length(label_order), name = "Set1")
+
+  df_counts <- data %>%
+    dplyr::filter(reads_group != "None") %>%
+    dplyr::group_by(sample, reads_group) %>%
+    dplyr::summarize(count = dplyr::n()) %>%
+    dplyr::ungroup()
+
+  ggplot2::ggplot(
+    df_counts,
+    ggplot2::aes(
+      x = sample,
+      y = count,
+      fill = reads_group
+    )
+  ) +
+    ggplot2::geom_bar(position = "stack", stat = "identity", width = 0.7) +
+    ggplot2::scale_fill_manual(
+      values = colors,
+      breaks = label_order,
+      name = "reads_group"
+    ) +
+    ggplot2::labs(x = "sample", y = "number of clonotypes") +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        angle = 90, vjust = 0.5, hjust = 1, size = 10
+      ),
+      axis.text.y = ggplot2::element_text(size = 10),
+      axis.title = ggplot2::element_text(size = 14),
+      legend.title = ggplot2::element_blank(),
+      legend.text = ggplot2::element_text(size = 12),
+      legend.position = "right",
+      panel.grid.major = ggplot2::element_blank(),
+      panel.grid.minor = ggplot2::element_blank(),
+      axis.line = ggplot2::element_line(color = "black"),
+      axis.text = ggplot2::element_text(margin = ggplot2::margin(t = 10)),
+      axis.ticks = ggplot2::element_line(color = "black", size = 0.3),
+      strip.background = ggplot2::element_blank(),
+      strip.text = ggplot2::element_text(size = 12)
+    ) +
+    ggplot2::scale_x_discrete(
+      labels = function(x) stringr::str_wrap(x, width = 10)
+    ) +
+    ggplot2::scale_y_continuous(expand = c(0, 0))
+}
diff --git a/R/plot_diversity_index.R b/R/utils-diversity-plot.R
similarity index 100%
rename from R/plot_diversity_index.R
rename to R/utils-diversity-plot.R
diff --git a/R/plot_motif_counts.R b/R/utils-motif-plot.R
similarity index 100%
rename from R/plot_motif_counts.R
rename to R/utils-motif-plot.R
diff --git a/man/plot_clonal_prop_per_group.Rd b/man/plot_clonal_prop_per_group.Rd
index 429ee8a..2014ca1 100644
--- a/man/plot_clonal_prop_per_group.Rd
+++ b/man/plot_clonal_prop_per_group.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_clonal_prop_per_group.R
+% Please edit documentation in R/utils-clonality-plot.R
 \name{plot_clonal_prop_per_group}
 \alias{plot_clonal_prop_per_group}
 \title{Plot clonal proportion per group}
diff --git a/man/plot_clonal_prop_per_sample.Rd b/man/plot_clonal_prop_per_sample.Rd
index 9844595..c21fe8e 100644
--- a/man/plot_clonal_prop_per_sample.Rd
+++ b/man/plot_clonal_prop_per_sample.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_clonal_prop_per_sample.R
+% Please edit documentation in R/utils-clonality-plot.R
 \name{plot_clonal_prop_per_sample}
 \alias{plot_clonal_prop_per_sample}
 \title{Plot clonal proportion per sample}
diff --git a/man/plot_clonotype_abundance.Rd b/man/plot_clonotype_abundance.Rd
index 689e369..3ee444f 100644
--- a/man/plot_clonotype_abundance.Rd
+++ b/man/plot_clonotype_abundance.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_clonotype_abundance.R
+% Please edit documentation in R/utils-clonality-plot.R
 \name{plot_clonotype_abundance}
 \alias{plot_clonotype_abundance}
 \title{Plot relative abundance for all clonotypes}
diff --git a/man/plot_diversity_index.Rd b/man/plot_diversity_index.Rd
index 2753e35..548c7ae 100644
--- a/man/plot_diversity_index.Rd
+++ b/man/plot_diversity_index.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_diversity_index.R
+% Please edit documentation in R/utils-diversity-plot.R
 \name{plot_diversity_index}
 \alias{plot_diversity_index}
 \title{Plot diversity index metrics}
diff --git a/man/plot_motif_counts.Rd b/man/plot_motif_counts.Rd
index 107c80b..21ab5a1 100644
--- a/man/plot_motif_counts.Rd
+++ b/man/plot_motif_counts.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_motif_counts.R
+% Please edit documentation in R/utils-motif-plot.R
 \name{plot_motif_counts}
 \alias{plot_motif_counts}
 \title{Plot Motif Counts}
diff --git a/man/plot_reads_group_abundance.Rd b/man/plot_reads_group_abundance.Rd
index 44d295a..019c27a 100644
--- a/man/plot_reads_group_abundance.Rd
+++ b/man/plot_reads_group_abundance.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_reads_group_abundance.R
+% Please edit documentation in R/utils-clonality-plot.R
 \name{plot_reads_group_abundance}
 \alias{plot_reads_group_abundance}
 \title{Plot reads group abundance for top 100 clonotypes}