diff --git a/NAMESPACE b/NAMESPACE
index ea22b809..69b807a3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -124,6 +124,8 @@ S3method(fortify_data_frame,Matrix)
 S3method(fortify_data_frame,character)
 S3method(fortify_data_frame,complex)
 S3method(fortify_data_frame,default)
+S3method(fortify_data_frame,dendrogram)
+S3method(fortify_data_frame,hclust)
 S3method(fortify_data_frame,logical)
 S3method(fortify_data_frame,matrix)
 S3method(fortify_data_frame,numeric)
@@ -409,7 +411,6 @@ export(continuous_limits)
 export(cross_link)
 export(cross_mark)
 export(cross_none)
-export(dendrogram_data)
 export(draw_key_draw)
 export(draw_key_draw2)
 export(element_curve)
diff --git a/R/align-dendrogram.R b/R/align-dendrogram.R
index 7688629c..f67f0305 100644
--- a/R/align-dendrogram.R
+++ b/R/align-dendrogram.R
@@ -16,35 +16,12 @@
 #' [`geom_segment`][ggplot2::geom_segment] layer with a data frame of the `edge`
 #' coordinates will be added when `plot_dendrogram = TRUE`.
 #'
-#' dendrogram `node` and `edge` contains following columns:
-#'
-#'   - `.panel`: Tree branch groups, used to create ggplot2 facet. Similar with
-#'              `panel` column, but always give the correct branch for usage of
-#'              the ggplot facet.
-#'  - `.names` and `.index`: a character names (only applicable when names
-#'    exists) and an integer index of the original data.
-#'   - `label`: node label text
-#'   - `x` and `y`: x-axis and y-axis coordinates for current node or the start
-#'                  node of the current edge.
-#'   - `xend` and `yend`: the x-axis and y-axis coordinates of the terminal node
-#'                        for current edge.
-#'   - `branch`: which branch current node or edge is. You can use this column
-#'               to color different groups.
-#'   - `leaf`: A logical value indicates whether current node is a leaf.
-#'   - `panel`: which panel current node is, if we split the plot into panel
-#'              using [`facet_grid`][ggplot2::facet_grid], this column will show
-#'              which panel current node or edge is from. Note: some nodes may
-#'              fall outside panel (between two panel), so there are possible
-#'              `NA` values in this column.
-#'   - `panel1` and `panel2`: The panel1 and panel2 variables have the same
-#'     functionality as `panel`, but they are specifically for the `edge` data
-#'     and correspond to both nodes of each edge.
-#'
+#' See [`fortify_data_frame.dendrogram()`] for details.
 #' @param merge_dendrogram A single boolean value, indicates whether we should
 #' merge multiple dendrograms, only used when previous groups have been
 #' established. Default: `FALSE`.
 #' @inheritParams align_hclust
-#' @inheritParams dendrogram_data
+#' @inheritParams fortify_data_frame.dendrogram
 #' @inheritParams ggalign
 #' @inheritSection align Discrete Axis Alignment
 #' @examples
@@ -173,7 +150,7 @@ AlignDendro <- ggproto("AlignDendro", AlignHclust,
                 tree <- .subset2(statistics, i)
                 n <- stats::nobs(tree)
                 end <- start + n
-                data[[i]] <- dendrogram_data(
+                data[[i]] <- fortify_data_frame(
                     tree,
                     priority = priority,
                     center = center,
@@ -186,11 +163,19 @@ AlignDendro <- ggproto("AlignDendro", AlignHclust,
                 )
                 start <- end
             }
-            data <- lapply(list_transpose(data), function(dat) {
-                ans <- vec_rbind(!!!dat, .names_to = "parent")
-                ans$ggpanel <- factor(.subset2(ans, "ggpanel"), branches)
-                ans
-            })
+            data <- lapply(
+                list(
+                    node = data,
+                    edge = lapply(data, ggalign_attr, "edge")
+                ),
+                function(dat) {
+                    ans <- vec_rbind(!!!dat, .names_to = "parent")
+                    ans$.panel <- factor(.subset2(ans, ".panel"), branches)
+                    ans
+                }
+            )
+            edge <- .subset2(data, "edge")
+            node <- .subset2(data, "node")
         } else {
             if (nlevels(panel) > 1L && type == "triangle" && self$in_linear) {
                 cli_warn(c(paste(
@@ -199,7 +184,7 @@ AlignDendro <- ggproto("AlignDendro", AlignHclust,
                 ), i = "will use {.filed rectangle} dendrogram instead"))
                 type <- "rectangle"
             }
-            data <- dendrogram_data(
+            data <- fortify_data_frame(
                 statistics,
                 priority = priority,
                 center = center,
@@ -210,11 +195,9 @@ AlignDendro <- ggproto("AlignDendro", AlignHclust,
                 root = root,
                 double = self$in_linear
             )
+            edge <- ggalign_attr(data, "edge")
+            node <- data
         }
-        node <- .subset2(data, "node")
-        edge <- .subset2(data, "edge")
-        node <- rename(node, c(ggpanel = ".panel", index = ".index"))
-        edge <- rename(edge, c(ggpanel = ".panel"))
 
         # add names
         if (!is.null(self$labels)) {
diff --git a/R/align-hclust.R b/R/align-hclust.R
index 17632e9e..a46a9c23 100644
--- a/R/align-hclust.R
+++ b/R/align-hclust.R
@@ -28,9 +28,7 @@
 #' (the height at which to cut the tree). By default,
 #' [`cutree()`][stats::cutree()] is used.
 #' @inheritSection align Discrete Axis Alignment
-#' @seealso
-#' - [`dendrogram_data()`]
-#' - [`hclust2()`]
+#' @seealso [`hclust2()`]
 #' @examples
 #' # align_hclust won't add a dendrogram
 #' ggheatmap(matrix(rnorm(81), nrow = 9)) +
diff --git a/R/align-phylo.R b/R/align-phylo.R
index 95f6a767..d5a128cc 100644
--- a/R/align-phylo.R
+++ b/R/align-phylo.R
@@ -182,15 +182,15 @@ AlignPhylo <- ggproto("AlignPhylo", Align,
     summary_align = function(self) c(TRUE, FALSE)
 )
 
-#' @inherit fortify_data_frame.default
-#' @inheritParams dendrogram_data
+#' @inherit fortify_data_frame.default title description
+#' @inheritParams rlang::args_dots_empty
+#' @inheritParams fortify_data_frame.dendrogram
 #' @param tree_type A single string, one of
 #' `r oxford_or(c("phylogram", "cladogram"))`, indicating the type of tree.
 #' Usually, you don't need to modify this.
 #' @param tip_pos The x-coordinates of the tip. Must be the same length
 #' of the number of tips in `tree`.
-#' @details
-#' A `data frame` with the node coordinates:
+#' @return A `data frame` with the node coordinates:
 #'   - `.index`: the original index in the tree for the the tip/node.
 #'   - `label`: the tip/node label text.
 #'   - `x` and `y`: x-axis and y-axis coordinates for the tip/node.
@@ -205,6 +205,7 @@ AlignPhylo <- ggproto("AlignPhylo", Align,
 fortify_data_frame.phylo <- function(data, ..., type = "rectangle",
                                      center = FALSE,
                                      tree_type = NULL, tip_pos = NULL) {
+    rlang::check_dots_empty()
     type <- arg_match0(type, c("rectangle", "triangle"))
     rectangle <- type == "rectangle"
     edge <- data$edge
diff --git a/R/dendrogram.R b/R/dendrogram.R
index 29f8d0c5..1ea9f7cc 100644
--- a/R/dendrogram.R
+++ b/R/dendrogram.R
@@ -109,10 +109,10 @@ make_dist <- function(matrix, distance, use_missing,
     d
 }
 
-#' Dengrogram x and y coordinates
+#' @inherit fortify_data_frame.default title description
 #'
-#' @param tree A [hclust][stats::hclust] or a [dendrogram][stats::as.dendrogram]
-#' object.
+#' @param data A [`hclust`][stats::hclust] or a
+#' [`dendrogram`][stats::as.dendrogram] object.
 #' @param priority A string of "left" or "right". if we draw from right to left,
 #' the left will override the right, so we take the `"left"` as the priority. If
 #' we draw from `left` to `right`, the right will override the left, so we take
@@ -135,50 +135,55 @@ make_dist <- function(matrix, distance, use_missing,
 #' should be doubled when segments span multiple branches. If `TRUE`, the
 #' horizontal lines will be repeated for each branch that the segment spans. If
 #' `FALSE`, only one horizontal line will be drawn.
-#' @return A list of 2 data.frame. One for node coordinates, another for edge
-#' coordinates.
-#' `node` and tree segments `edge` coordinates contains following columns:
-#'   - `index`: the original index in the tree for the current node
+#' @return A `data frame` with the node coordinates:
+#'   - `.panel`: Similar with `panel` column, but always give the correct
+#'              branch for usage of the ggplot facet.
+#'   - `.index`: the original index in the tree for the the node
 #'   - `label`: node label text
-#'   - `x` and `y`: x-axis and y-axis coordinates for current node or the start
-#'                  node of the current edge.
-#'   - `xend` and `yend`: the x-axis and y-axis coordinates of the terminal node
-#'                        for current edge.
-#'   - `branch`: which branch current node or edge is. You can use this column
-#'               to color different groups.
-#'   - `panel`: which panel current node is, if we split the plot into panel
+#'   - `x` and `y`: x-axis and y-axis coordinates for the node
+#'   - `branch`: which branch the node is. You can use this column to color
+#'               different groups.
+#'   - `panel`: which panel the node is, if we split the plot into panel
 #'              using [facet_grid][ggplot2::facet_grid], this column will show
-#'              which panel current node or edge is from. Note: some nodes may
+#'              which panel the node is from. Note: some nodes may
 #'              fall outside panel (between two panels), so there are possible
 #'              `NA` values in this column.
-#'   - `ggpanel`: Similar with `panel` column, but always give the correct
+#'   - `leaf`: A logical value indicates whether the node is a leaf.
+#' @section ggalign attributes:
+#'  `edge`: A `data frame` for edge coordinates:
+#'  - `.panel`: Similar with `panel` column, but always give the correct
 #'              branch for usage of the ggplot facet.
-#'   - `panel1` and `panel2`: The panel1 and panel2 variables have the same
+#'  - `x` and `y`: x-axis and y-axis coordinates for the start node of the edge.
+#'  - `xend` and `yend`: the x-axis and y-axis coordinates of the terminal node
+#'                       for edge.
+#'  - `branch`: which branch the edge is. You can use this column to color
+#'              different groups.
+#'  - `panel1` and `panel2`: The panel1 and panel2 columns have the same
 #'     functionality as `panel`, but they are specifically for the `edge` data
 #'     and correspond to both nodes of each edge.
-#'   - `leaf`: A logical value indicates whether current node is a leaf.
 #' @examples
-#' dendrogram_data(hclust(dist(USArrests), "ave"))
+#' fortify_data_frame(hclust(dist(USArrests), "ave"))
 #' @importFrom grid is.unit
 #' @importFrom stats order.dendrogram
 #' @importFrom rlang arg_match0
+#' @family fortify_data_frame methods
 #' @export
-dendrogram_data <- function(tree,
-                            priority = "right",
-                            center = FALSE,
-                            type = "rectangle",
-                            leaf_pos = NULL,
-                            leaf_braches = NULL,
-                            reorder_branches = TRUE,
-                            branch_gap = NULL,
-                            root = NULL,
-                            double = TRUE) {
-    dend <- check_dendrogram(tree)
+fortify_data_frame.dendrogram <- function(data, ...,
+                                          priority = "right",
+                                          center = FALSE,
+                                          type = "rectangle",
+                                          leaf_pos = NULL,
+                                          leaf_braches = NULL,
+                                          reorder_branches = TRUE,
+                                          branch_gap = NULL,
+                                          root = NULL,
+                                          double = TRUE) {
+    rlang::check_dots_empty()
     assert_bool(center)
     assert_bool(reorder_branches)
     type <- arg_match0(type, c("rectangle", "triangle"))
     priority <- arg_match0(priority, c("left", "right"))
-    N <- stats::nobs(dend)
+    N <- stats::nobs(data)
     rectangle <- type == "rectangle"
     if (is.null(leaf_pos)) {
         leaf_pos <- seq_len(N)
@@ -209,7 +214,7 @@ dendrogram_data <- function(tree,
     }
 
     if (!is.null(leaf_braches) && reorder_branches) {
-        leaf_braches <- .subset(leaf_braches, order.dendrogram(dend))
+        leaf_braches <- .subset(leaf_braches, order.dendrogram(data))
     }
 
     # check `branch_gap`
@@ -239,7 +244,7 @@ dendrogram_data <- function(tree,
     branch_levels <- NULL
     last_branch <- root
     total_gap <- 0
-    .dendrogram_data <- function(dend, from_root = TRUE) {
+    dendrogram_data <- function(dend, from_root = TRUE) {
         if (stats::is.leaf(dend)) { # base version
             index <- as.integer(dend) # the column index of the original data
             y <- attr(dend, "height") %||% 0
@@ -282,7 +287,7 @@ dendrogram_data <- function(tree,
 
             # for the children nodes ---------------------------------
             data <- list_transpose(
-                lapply(dend, .dendrogram_data, from_root = FALSE)
+                lapply(dend, dendrogram_data, from_root = FALSE)
             )
 
             # node should be the direct children
@@ -444,7 +449,7 @@ dendrogram_data <- function(tree,
             cli_abort("{.arg dend} must be a {.cls dendrogram} object")
         }
     }
-    ans <- .dendrogram_data(dend)
+    ans <- dendrogram_data(data)
     node <- .subset2(ans, "node")
     edge <- .subset2(ans, "edge")
 
@@ -460,7 +465,16 @@ dendrogram_data <- function(tree,
         edge$branch <- factor(.subset2(edge, "branch"), branch_levels)
         edge$ggpanel <- factor(.subset2(edge, "ggpanel"), panel_levels)
     }
-    list(node = node, edge = edge)
+    node <- rename(node, c(ggpanel = ".panel", index = ".index"))
+    edge <- rename(edge, c(ggpanel = ".panel"))
+    ggalign_attr_set(node, list(edge = edge))
+}
+
+#' @param ... Additional arguments passed to `dendrogram` method.
+#' @export
+#' @rdname fortify_data_frame.dendrogram
+fortify_data_frame.hclust <- function(data, ...) {
+    fortify_data_frame.dendrogram(stats::as.dendrogram(data), ...)
 }
 
 #' @param ggpanels Won't be `NA`
@@ -584,18 +598,3 @@ tree_branch_heights <- function(dend) {
         )
     }
 }
-
-#' @importFrom rlang caller_arg caller_env
-check_dendrogram <- function(tree, arg = caller_arg(tree),
-                             call = caller_call()) {
-    if (inherits(tree, "hclust")) {
-        stats::as.dendrogram(tree)
-    } else if (inherits(tree, "dendrogram")) {
-        tree
-    } else {
-        cli_abort(paste(
-            "{.arg {arg}} must be a {.cls hclust}",
-            "or a {.cls dendrogram} object."
-        ), call = call)
-    }
-}
diff --git a/R/fortify-data-frame.R b/R/fortify-data-frame.R
index 9d6969b3..a286eba6 100644
--- a/R/fortify-data-frame.R
+++ b/R/fortify-data-frame.R
@@ -6,20 +6,20 @@
 #' This function converts various objects to a data frame.
 #'
 #' @param data An object to be converted to a data frame.
-#' @inheritParams rlang::args_dots_used
+#' @param ... Arguments passed to methods.
 #' @return A data frame.
 #' @seealso
 #' - [`fortify_data_frame.default()`]
-#' - [`fortify_data_frame.character()`]
-#' - [`fortify_data_frame.numeric()`]
+#' - [`fortify_data_frame.character()`]/[`fortify_data_frame.numeric()`]
 #' - [`fortify_data_frame.matrix()`]
+#' - [`fortify_data_frame.dendrogram()`]
 #' @export
 fortify_data_frame <- function(data, ...) {
-    rlang::check_dots_used()
     UseMethod("fortify_data_frame")
 }
 
 #' @inherit fortify_data_frame
+#' @param ... Additional arguments passed to [`fortify()`][ggplot2::fortify].
 #' @details
 #' By default, it calls [`fortify()`][ggplot2::fortify] to build the
 #' data frame.
@@ -29,10 +29,10 @@ fortify_data_frame.default <- function(data, ...) {
     ggplot2::fortify(model = data, ...)
 }
 
-#' @inherit fortify_data_frame.default
-#' @details
-#' When `data` is an atomic vector, it'll be converted to a data frame with
-#' following columns:
+#' @inherit fortify_data_frame.default title description
+#' @param data An object to be converted to a data frame.
+#' @inheritParams rlang::args_dots_empty
+#' @return A data frame with following columns:
 #'
 #'  - `.names`: the names for the vector (only applicable if names exist).
 #'  - `value`: the actual value of the vector.
@@ -40,34 +40,37 @@ fortify_data_frame.default <- function(data, ...) {
 #' @family fortify_data_frame methods
 #' @export
 fortify_data_frame.character <- function(data, ...) {
+    rlang::check_dots_empty()
     ans <- list(.names = vec_names(data), value = data)
     if (is.null(.subset2(ans, ".names"))) ans$.names <- NULL
     new_data_frame(ans)
 }
 
-#' @inherit fortify_data_frame.character
-#' @family fortify_data_frame methods
+#' @rdname fortify_data_frame.character
 #' @export
 fortify_data_frame.numeric <- fortify_data_frame.character
 
-#' @inherit fortify_data_frame.character
-#' @family fortify_data_frame methods
+#' @rdname fortify_data_frame.character
 #' @export
 fortify_data_frame.logical <- fortify_data_frame.character
 
-#' @inherit fortify_data_frame.character
-#' @family fortify_data_frame methods
+#' @rdname fortify_data_frame.character
 #' @export
 fortify_data_frame.complex <- fortify_data_frame.character
 
 #' @export
-fortify_data_frame.waiver <- function(data, ...) data
+fortify_data_frame.waiver <- function(data, ...) {
+    rlang::check_dots_empty()
+    data
+}
 
 #' @export
-fortify_data_frame.NULL <- function(data, ...) data
+fortify_data_frame.NULL <- fortify_data_frame.waiver
 
-#' @inherit fortify_data_frame.default
-#' @details
+#' @inherit fortify_data_frame.default title description
+#' @param data A matrix-like object.
+#' @inheritParams rlang::args_dots_empty
+#' @return
 #' Matrix will be transformed into a long-form data frame, where each row
 #' represents a unique combination of matrix indices and their corresponding
 #' values. The resulting data frame will contain the following columns:
@@ -83,6 +86,7 @@ fortify_data_frame.NULL <- function(data, ...) data
 #' @family fortify_data_frame methods
 #' @export
 fortify_data_frame.matrix <- function(data, ...) {
+    rlang::check_dots_empty()
     row_nms <- vec_names(data)
     col_nms <- colnames(data)
     data <- new_data_frame(list(
@@ -98,11 +102,11 @@ fortify_data_frame.matrix <- function(data, ...) {
 #' @export
 #' @rdname fortify_data_frame.matrix
 fortify_data_frame.DelayedMatrix <- function(data, ...) {
-    fortify_data_frame(as.matrix(data))
+    fortify_data_frame(as.matrix(data), ...)
 }
 
 #' @export
 #' @rdname fortify_data_frame.matrix
 fortify_data_frame.Matrix <- function(data, ...) {
-    fortify_data_frame(as.matrix(data))
+    fortify_data_frame(as.matrix(data), ...)
 }
diff --git a/R/fortify-matrix.R b/R/fortify-matrix.R
index a6a65b22..082f47d3 100644
--- a/R/fortify-matrix.R
+++ b/R/fortify-matrix.R
@@ -6,7 +6,7 @@
 #' This function converts various objects into a matrix format.
 #'
 #' @param data An object to be converted to a matrix.
-#' @inheritParams rlang::args_dots_used
+#' @param ... Arguments passed to methods.
 #' @return A matrix.
 #' @seealso
 #' - [`fortify_matrix.default()`]
@@ -14,17 +14,19 @@
 #' - [`fortify_matrix.GISTIC()`]
 #' @export
 fortify_matrix <- function(data, ...) {
-    rlang::check_dots_used()
     UseMethod("fortify_matrix")
 }
 
-#' @inherit fortify_matrix
-#' @description
+#' @inherit fortify_matrix title description return
+#' @inheritParams rlang::args_dots_empty
+#' @inheritParams fortify_matrix
+#' @details
 #' By default, it calls [`as.matrix()`] to build a matrix.
 #' @family fortify_matrix methods
 #' @importFrom rlang try_fetch
 #' @export
 fortify_matrix.default <- function(data, ...) {
+    rlang::check_dots_empty()
     try_fetch(
         as.matrix(data),
         error = function(cnd) {
@@ -38,23 +40,29 @@ fortify_matrix.default <- function(data, ...) {
 }
 
 #' @export
-fortify_matrix.matrix <- function(data, ...) data
+fortify_matrix.matrix <- function(data, ...) {
+    rlang::check_dots_empty()
+    data
+}
 
 #' @export
-fortify_matrix.waiver <- function(data, ...) data
+fortify_matrix.waiver <- fortify_matrix.matrix
 
 #' @export
-fortify_matrix.NULL <- function(data, ...) NULL
+fortify_matrix.NULL <- fortify_matrix.matrix
 
 #' @export
-fortify_matrix.function <- function(data, ...) data
+fortify_matrix.function <- fortify_matrix.matrix
 
 #' @export
-fortify_matrix.formula <- function(data, ...) rlang::as_function(data)
+fortify_matrix.formula <- function(data, ...) {
+    rlang::check_dots_empty()
+    rlang::as_function(data)
+}
 
-#' @inherit fortify_matrix
-#' @inheritParams fortify_matrix.default
-#' @param ... Not used currently.
+#' @inherit fortify_matrix title description return
+#' @param data A [`MAF`][maftools::read.maf] object.
+#' @inheritParams rlang::args_dots_empty
 #' @param genes An atomic character defines the genes to draw.
 #' @param n_top A single number indicates how many top genes to be drawn.
 #' @param remove_empty_samples A single boolean value indicating whether to drop
@@ -84,6 +92,7 @@ fortify_matrix.MAF <- function(data, ..., genes = NULL, n_top = NULL,
                                remove_empty_samples = TRUE,
                                collapse_vars = TRUE,
                                use_syn = TRUE) {
+    rlang::check_dots_empty()
     rlang::check_installed(
         "maftools", "to make alterations matrix from `MAF` object"
     )
@@ -240,9 +249,9 @@ fortify_matrix.MAF <- function(data, ..., genes = NULL, n_top = NULL,
     ))
 }
 
-#' @inherit fortify_matrix
-#' @inheritParams fortify_matrix.default
-#' @param ... Not used currently.
+#' @inherit fortify_matrix title description return
+#' @inheritParams rlang::args_dots_empty
+#' @param data A [`GISTIC`][maftools::readGistic] object.
 #' @param n_top A single number indicates how many top bands to be drawn.
 #' @param bands An atomic character defines the bands to draw.
 #' @param ignored_bands An atomic character defines the bands to be ignored.
@@ -264,6 +273,7 @@ fortify_matrix.MAF <- function(data, ..., genes = NULL, n_top = NULL,
 fortify_matrix.GISTIC <- function(data, ..., n_top = NULL, bands = NULL,
                                   ignored_bands = NULL, sample_anno = NULL,
                                   remove_empty_samples = TRUE) {
+    rlang::check_dots_empty()
     rlang::check_installed(
         "maftools",
         "to make CNV matrix from `GISTIC` object"
diff --git a/man/align_dendro.Rd b/man/align_dendro.Rd
index 49cb37c2..203b21e0 100644
--- a/man/align_dendro.Rd
+++ b/man/align_dendro.Rd
@@ -125,30 +125,7 @@ in \code{\link[=ggalign_attr]{ggalign}} attribute, in addition, a
 \code{\link[ggplot2:geom_segment]{geom_segment}} layer with a data frame of the \code{edge}
 coordinates will be added when \code{plot_dendrogram = TRUE}.
 
-dendrogram \code{node} and \code{edge} contains following columns:
-\itemize{
-\item \code{.panel}: Tree branch groups, used to create ggplot2 facet. Similar with
-\code{panel} column, but always give the correct branch for usage of
-the ggplot facet.
-\item \code{.names} and \code{.index}: a character names (only applicable when names
-exists) and an integer index of the original data.
-\item \code{label}: node label text
-\item \code{x} and \code{y}: x-axis and y-axis coordinates for current node or the start
-node of the current edge.
-\item \code{xend} and \code{yend}: the x-axis and y-axis coordinates of the terminal node
-for current edge.
-\item \code{branch}: which branch current node or edge is. You can use this column
-to color different groups.
-\item \code{leaf}: A logical value indicates whether current node is a leaf.
-\item \code{panel}: which panel current node is, if we split the plot into panel
-using \code{\link[ggplot2:facet_grid]{facet_grid}}, this column will show
-which panel current node or edge is from. Note: some nodes may
-fall outside panel (between two panel), so there are possible
-\code{NA} values in this column.
-\item \code{panel1} and \code{panel2}: The panel1 and panel2 variables have the same
-functionality as \code{panel}, but they are specifically for the \code{edge} data
-and correspond to both nodes of each edge.
-}
+See \code{\link[=fortify_data_frame.dendrogram]{fortify_data_frame.dendrogram()}} for details.
 }
 
 \section{Discrete Axis Alignment}{
diff --git a/man/align_hclust.Rd b/man/align_hclust.Rd
index 44c82072..5380e0fa 100644
--- a/man/align_hclust.Rd
+++ b/man/align_hclust.Rd
@@ -89,8 +89,5 @@ ggheatmap(matrix(rnorm(81), nrow = 9)) +
     align_hclust(k = 3L)
 }
 \seealso{
-\itemize{
-\item \code{\link[=dendrogram_data]{dendrogram_data()}}
-\item \code{\link[=hclust2]{hclust2()}}
-}
+\code{\link[=hclust2]{hclust2()}}
 }
diff --git a/man/fortify_data_frame.Rd b/man/fortify_data_frame.Rd
index 8095730e..13bd8313 100644
--- a/man/fortify_data_frame.Rd
+++ b/man/fortify_data_frame.Rd
@@ -22,8 +22,8 @@ This function converts various objects to a data frame.
 \seealso{
 \itemize{
 \item \code{\link[=fortify_data_frame.default]{fortify_data_frame.default()}}
-\item \code{\link[=fortify_data_frame.character]{fortify_data_frame.character()}}
-\item \code{\link[=fortify_data_frame.numeric]{fortify_data_frame.numeric()}}
+\item \code{\link[=fortify_data_frame.character]{fortify_data_frame.character()}}/\code{\link[=fortify_data_frame.numeric]{fortify_data_frame.numeric()}}
 \item \code{\link[=fortify_data_frame.matrix]{fortify_data_frame.matrix()}}
+\item \code{\link[=fortify_data_frame.dendrogram]{fortify_data_frame.dendrogram()}}
 }
 }
diff --git a/man/fortify_data_frame.character.Rd b/man/fortify_data_frame.character.Rd
index d76daf7d..611ef32b 100644
--- a/man/fortify_data_frame.character.Rd
+++ b/man/fortify_data_frame.character.Rd
@@ -2,37 +2,40 @@
 % Please edit documentation in R/fortify-data-frame.R
 \name{fortify_data_frame.character}
 \alias{fortify_data_frame.character}
+\alias{fortify_data_frame.numeric}
+\alias{fortify_data_frame.logical}
+\alias{fortify_data_frame.complex}
 \title{Build a data frame}
 \usage{
 \method{fortify_data_frame}{character}(data, ...)
+
+\method{fortify_data_frame}{numeric}(data, ...)
+
+\method{fortify_data_frame}{logical}(data, ...)
+
+\method{fortify_data_frame}{complex}(data, ...)
 }
 \arguments{
 \item{data}{An object to be converted to a data frame.}
 
-\item{...}{Arguments passed to methods.}
+\item{...}{These dots are for future extensions and must be empty.}
 }
 \value{
-A data frame.
+A data frame with following columns:
+\itemize{
+\item \code{.names}: the names for the vector (only applicable if names exist).
+\item \code{value}: the actual value of the vector.
+}
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 
 This function converts various objects to a data frame.
 }
-\details{
-When \code{data} is an atomic vector, it'll be converted to a data frame with
-following columns:
-\itemize{
-\item \code{.names}: the names for the vector (only applicable if names exist).
-\item \code{value}: the actual value of the vector.
-}
-}
 \seealso{
 Other fortify_data_frame methods: 
-\code{\link{fortify_data_frame.complex}()},
 \code{\link{fortify_data_frame.default}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.matrix}()},
-\code{\link{fortify_data_frame.numeric}()}
+\code{\link{fortify_data_frame.dendrogram}()},
+\code{\link{fortify_data_frame.matrix}()}
 }
 \concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.complex.Rd b/man/fortify_data_frame.complex.Rd
deleted file mode 100644
index 5d63d44d..00000000
--- a/man/fortify_data_frame.complex.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fortify-data-frame.R
-\name{fortify_data_frame.complex}
-\alias{fortify_data_frame.complex}
-\title{Build a data frame}
-\usage{
-\method{fortify_data_frame}{complex}(data, ...)
-}
-\arguments{
-\item{data}{An object to be converted to a data frame.}
-
-\item{...}{Arguments passed to methods.}
-}
-\value{
-A data frame.
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-This function converts various objects to a data frame.
-}
-\details{
-When \code{data} is an atomic vector, it'll be converted to a data frame with
-following columns:
-\itemize{
-\item \code{.names}: the names for the vector (only applicable if names exist).
-\item \code{value}: the actual value of the vector.
-}
-}
-\seealso{
-Other fortify_data_frame methods: 
-\code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.default}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.matrix}()},
-\code{\link{fortify_data_frame.numeric}()}
-}
-\concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.default.Rd b/man/fortify_data_frame.default.Rd
index 04f4529d..63d7a40d 100644
--- a/man/fortify_data_frame.default.Rd
+++ b/man/fortify_data_frame.default.Rd
@@ -9,7 +9,7 @@
 \arguments{
 \item{data}{An object to be converted to a data frame.}
 
-\item{...}{Arguments passed to methods.}
+\item{...}{Additional arguments passed to \code{\link[ggplot2:fortify]{fortify()}}.}
 }
 \value{
 A data frame.
@@ -26,9 +26,7 @@ data frame.
 \seealso{
 Other fortify_data_frame methods: 
 \code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.complex}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.matrix}()},
-\code{\link{fortify_data_frame.numeric}()}
+\code{\link{fortify_data_frame.dendrogram}()},
+\code{\link{fortify_data_frame.matrix}()}
 }
 \concept{fortify_data_frame methods}
diff --git a/man/dendrogram_data.Rd b/man/fortify_data_frame.dendrogram.Rd
similarity index 54%
rename from man/dendrogram_data.Rd
rename to man/fortify_data_frame.dendrogram.Rd
index 0be9fecb..6c7cef46 100644
--- a/man/dendrogram_data.Rd
+++ b/man/fortify_data_frame.dendrogram.Rd
@@ -1,11 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/dendrogram.R
-\name{dendrogram_data}
-\alias{dendrogram_data}
-\title{Dengrogram x and y coordinates}
+\name{fortify_data_frame.dendrogram}
+\alias{fortify_data_frame.dendrogram}
+\alias{fortify_data_frame.hclust}
+\title{Build a data frame}
 \usage{
-dendrogram_data(
-  tree,
+\method{fortify_data_frame}{dendrogram}(
+  data,
+  ...,
   priority = "right",
   center = FALSE,
   type = "rectangle",
@@ -16,10 +18,14 @@ dendrogram_data(
   root = NULL,
   double = TRUE
 )
+
+\method{fortify_data_frame}{hclust}(data, ...)
 }
 \arguments{
-\item{tree}{A \link[stats:hclust]{hclust} or a \link[stats:dendrogram]{dendrogram}
-object.}
+\item{data}{A \code{\link[stats:hclust]{hclust}} or a
+\code{\link[stats:dendrogram]{dendrogram}} object.}
+
+\item{...}{Additional arguments passed to \code{dendrogram} method.}
 
 \item{priority}{A string of "left" or "right". if we draw from right to left,
 the left will override the right, so we take the \code{"left"} as the priority. If
@@ -53,34 +59,52 @@ horizontal lines will be repeated for each branch that the segment spans. If
 \code{FALSE}, only one horizontal line will be drawn.}
 }
 \value{
-A list of 2 data.frame. One for node coordinates, another for edge
-coordinates.
-\code{node} and tree segments \code{edge} coordinates contains following columns:
+A \verb{data frame} with the node coordinates:
 \itemize{
-\item \code{index}: the original index in the tree for the current node
+\item \code{.panel}: Similar with \code{panel} column, but always give the correct
+branch for usage of the ggplot facet.
+\item \code{.index}: the original index in the tree for the the node
 \item \code{label}: node label text
-\item \code{x} and \code{y}: x-axis and y-axis coordinates for current node or the start
-node of the current edge.
-\item \code{xend} and \code{yend}: the x-axis and y-axis coordinates of the terminal node
-for current edge.
-\item \code{branch}: which branch current node or edge is. You can use this column
-to color different groups.
-\item \code{panel}: which panel current node is, if we split the plot into panel
+\item \code{x} and \code{y}: x-axis and y-axis coordinates for the node
+\item \code{branch}: which branch the node is. You can use this column to color
+different groups.
+\item \code{panel}: which panel the node is, if we split the plot into panel
 using \link[ggplot2:facet_grid]{facet_grid}, this column will show
-which panel current node or edge is from. Note: some nodes may
+which panel the node is from. Note: some nodes may
 fall outside panel (between two panels), so there are possible
 \code{NA} values in this column.
-\item \code{ggpanel}: Similar with \code{panel} column, but always give the correct
+\item \code{leaf}: A logical value indicates whether the node is a leaf.
+}
+}
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+
+This function converts various objects to a data frame.
+}
+\section{ggalign attributes}{
+
+\code{edge}: A \verb{data frame} for edge coordinates:
+\itemize{
+\item \code{.panel}: Similar with \code{panel} column, but always give the correct
 branch for usage of the ggplot facet.
-\item \code{panel1} and \code{panel2}: The panel1 and panel2 variables have the same
+\item \code{x} and \code{y}: x-axis and y-axis coordinates for the start node of the edge.
+\item \code{xend} and \code{yend}: the x-axis and y-axis coordinates of the terminal node
+for edge.
+\item \code{branch}: which branch the edge is. You can use this column to color
+different groups.
+\item \code{panel1} and \code{panel2}: The panel1 and panel2 columns have the same
 functionality as \code{panel}, but they are specifically for the \code{edge} data
 and correspond to both nodes of each edge.
-\item \code{leaf}: A logical value indicates whether current node is a leaf.
 }
 }
-\description{
-Dengrogram x and y coordinates
-}
+
 \examples{
-dendrogram_data(hclust(dist(USArrests), "ave"))
+fortify_data_frame(hclust(dist(USArrests), "ave"))
+}
+\seealso{
+Other fortify_data_frame methods: 
+\code{\link{fortify_data_frame.character}()},
+\code{\link{fortify_data_frame.default}()},
+\code{\link{fortify_data_frame.matrix}()}
 }
+\concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.logical.Rd b/man/fortify_data_frame.logical.Rd
deleted file mode 100644
index 9387c21d..00000000
--- a/man/fortify_data_frame.logical.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fortify-data-frame.R
-\name{fortify_data_frame.logical}
-\alias{fortify_data_frame.logical}
-\title{Build a data frame}
-\usage{
-\method{fortify_data_frame}{logical}(data, ...)
-}
-\arguments{
-\item{data}{An object to be converted to a data frame.}
-
-\item{...}{Arguments passed to methods.}
-}
-\value{
-A data frame.
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-This function converts various objects to a data frame.
-}
-\details{
-When \code{data} is an atomic vector, it'll be converted to a data frame with
-following columns:
-\itemize{
-\item \code{.names}: the names for the vector (only applicable if names exist).
-\item \code{value}: the actual value of the vector.
-}
-}
-\seealso{
-Other fortify_data_frame methods: 
-\code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.complex}()},
-\code{\link{fortify_data_frame.default}()},
-\code{\link{fortify_data_frame.matrix}()},
-\code{\link{fortify_data_frame.numeric}()}
-}
-\concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.matrix.Rd b/man/fortify_data_frame.matrix.Rd
index 2668e648..b5e4a6bf 100644
--- a/man/fortify_data_frame.matrix.Rd
+++ b/man/fortify_data_frame.matrix.Rd
@@ -13,19 +13,11 @@
 \method{fortify_data_frame}{Matrix}(data, ...)
 }
 \arguments{
-\item{data}{An object to be converted to a data frame.}
+\item{data}{A matrix-like object.}
 
-\item{...}{Arguments passed to methods.}
+\item{...}{These dots are for future extensions and must be empty.}
 }
 \value{
-A data frame.
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-This function converts various objects to a data frame.
-}
-\details{
 Matrix will be transformed into a long-form data frame, where each row
 represents a unique combination of matrix indices and their corresponding
 values. The resulting data frame will contain the following columns:
@@ -37,12 +29,15 @@ when names exist) and column index of the original matrix.
 \item \code{value}: the actual value.
 }
 }
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+
+This function converts various objects to a data frame.
+}
 \seealso{
 Other fortify_data_frame methods: 
 \code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.complex}()},
 \code{\link{fortify_data_frame.default}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.numeric}()}
+\code{\link{fortify_data_frame.dendrogram}()}
 }
 \concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.numeric.Rd b/man/fortify_data_frame.numeric.Rd
deleted file mode 100644
index 462d225e..00000000
--- a/man/fortify_data_frame.numeric.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fortify-data-frame.R
-\name{fortify_data_frame.numeric}
-\alias{fortify_data_frame.numeric}
-\title{Build a data frame}
-\usage{
-\method{fortify_data_frame}{numeric}(data, ...)
-}
-\arguments{
-\item{data}{An object to be converted to a data frame.}
-
-\item{...}{Arguments passed to methods.}
-}
-\value{
-A data frame.
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-This function converts various objects to a data frame.
-}
-\details{
-When \code{data} is an atomic vector, it'll be converted to a data frame with
-following columns:
-\itemize{
-\item \code{.names}: the names for the vector (only applicable if names exist).
-\item \code{value}: the actual value of the vector.
-}
-}
-\seealso{
-Other fortify_data_frame methods: 
-\code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.complex}()},
-\code{\link{fortify_data_frame.default}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.matrix}()}
-}
-\concept{fortify_data_frame methods}
diff --git a/man/fortify_data_frame.phylo.Rd b/man/fortify_data_frame.phylo.Rd
index 70990d14..f666cba5 100644
--- a/man/fortify_data_frame.phylo.Rd
+++ b/man/fortify_data_frame.phylo.Rd
@@ -14,9 +14,10 @@
 )
 }
 \arguments{
-\item{data}{An object to be converted to a data frame.}
+\item{data}{A \code{\link[stats:hclust]{hclust}} or a
+\code{\link[stats:dendrogram]{dendrogram}} object.}
 
-\item{...}{Arguments passed to methods.}
+\item{...}{These dots are for future extensions and must be empty.}
 
 \item{type}{A string indicates the plot type, \code{"rectangle"} or \code{"triangle"}.}
 
@@ -32,14 +33,6 @@ Usually, you don't need to modify this.}
 of the number of tips in \code{tree}.}
 }
 \value{
-A data frame.
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-
-This function converts various objects to a data frame.
-}
-\details{
 A \verb{data frame} with the node coordinates:
 \itemize{
 \item \code{.index}: the original index in the tree for the the tip/node.
@@ -48,6 +41,11 @@ A \verb{data frame} with the node coordinates:
 \item \code{tip}: A logical value indicates whether current node is a tip.
 }
 }
+\description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+
+This function converts various objects to a data frame.
+}
 \section{ggalign attributes}{
 
 \code{edge}: A \verb{data frame} for edge coordinates:
@@ -58,11 +56,3 @@ for edge.
 }
 }
 
-\seealso{
-Other fortify_data_frame methods: 
-\code{\link{fortify_data_frame.character}()},
-\code{\link{fortify_data_frame.complex}()},
-\code{\link{fortify_data_frame.logical}()},
-\code{\link{fortify_data_frame.matrix}()},
-\code{\link{fortify_data_frame.numeric}()}
-}
diff --git a/man/fortify_matrix.GISTIC.Rd b/man/fortify_matrix.GISTIC.Rd
index 94a16895..eedf228b 100644
--- a/man/fortify_matrix.GISTIC.Rd
+++ b/man/fortify_matrix.GISTIC.Rd
@@ -15,9 +15,9 @@
 )
 }
 \arguments{
-\item{data}{An object to be converted to a matrix.}
+\item{data}{A \code{\link[maftools:readGistic]{GISTIC}} object.}
 
-\item{...}{Not used currently.}
+\item{...}{These dots are for future extensions and must be empty.}
 
 \item{n_top}{A single number indicates how many top bands to be drawn.}
 
diff --git a/man/fortify_matrix.MAF.Rd b/man/fortify_matrix.MAF.Rd
index 38038a3e..de84eff8 100644
--- a/man/fortify_matrix.MAF.Rd
+++ b/man/fortify_matrix.MAF.Rd
@@ -15,9 +15,9 @@
 )
 }
 \arguments{
-\item{data}{An object to be converted to a matrix.}
+\item{data}{A \code{\link[maftools:read.maf]{MAF}} object.}
 
-\item{...}{Not used currently.}
+\item{...}{These dots are for future extensions and must be empty.}
 
 \item{genes}{An atomic character defines the genes to draw.}
 
diff --git a/man/fortify_matrix.default.Rd b/man/fortify_matrix.default.Rd
index 9a2ce110..7424b2d1 100644
--- a/man/fortify_matrix.default.Rd
+++ b/man/fortify_matrix.default.Rd
@@ -15,6 +15,11 @@
 A matrix.
 }
 \description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+
+This function converts various objects into a matrix format.
+}
+\details{
 By default, it calls \code{\link[=as.matrix]{as.matrix()}} to build a matrix.
 }
 \seealso{