deleted file mode 100644

@@ -1,210 +0,0 @@

-\name{Heatmap}

-\alias{Heatmap}

-\title{

-Constructor method for Heatmap class

-}

-\description{

-Constructor method for Heatmap class

-}

-\usage{

-Heatmap(matrix, col, name,

-    na_col = "grey",

-    color_space = "LAB",

-    rect_gp = gpar(col = NA),

-    border = NA,

-    cell_fun = NULL,

-    layer_fun = NULL,

-    jitter = FALSE,

-    

-    row_title = character(0),

-    row_title_side = c("left", "right"),

-    row_title_gp = gpar(fontsize = 14),

-    row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),

-    column_title = character(0),

-    column_title_side = c("top", "bottom"),

-    column_title_gp = gpar(fontsize = 14),

-    column_title_rot = 0,

-    

-    cluster_rows = TRUE,

-    cluster_row_slices = TRUE,

-    clustering_distance_rows = "euclidean",

-    clustering_method_rows = "complete",

-    row_dend_side = c("left", "right"),

-    row_dend_width = unit(10, "mm"),

-    show_row_dend = TRUE,

-    row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

-    row_dend_gp = gpar(),

-    cluster_columns = TRUE,

-    cluster_column_slices = TRUE,

-    clustering_distance_columns = "euclidean",

-    clustering_method_columns = "complete",

-    column_dend_side = c("top", "bottom"),

-    column_dend_height = unit(10, "mm"),

-    show_column_dend = TRUE,

-    column_dend_gp = gpar(),

-    column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns),

-    

-    row_order = NULL,

-    column_order = NULL,

-    

-    row_labels = rownames(matrix),

-    row_names_side = c("right", "left"),

-    show_row_names = TRUE,

-    row_names_max_width = unit(6, "cm"),

-    row_names_gp = gpar(fontsize = 12),

-    row_names_rot = 0,

-    row_names_centered = FALSE,

-    column_labels = colnames(matrix),

-    column_names_side = c("bottom", "top"),

-    show_column_names = TRUE,

-    column_names_max_height = unit(6, "cm"),

-    column_names_gp = gpar(fontsize = 12),

-    column_names_rot = 90,

-    column_names_centered = FALSE,

-    

-    top_annotation = NULL,

-    bottom_annotation = NULL,

-    left_annotation = NULL,

-    right_annotation = NULL,

-    

-    km = 1,

-    split = NULL,

-    row_km = km,

-    row_km_repeats = 1,

-    row_split = split,

-    column_km = 1,

-    column_km_repeats = 1,

-    column_split = NULL,

-    gap = unit(1, "mm"),

-    row_gap = unit(1, "mm"),

-    column_gap = unit(1, "mm"),

-    show_parent_dend_line = ht_opt$show_parent_dend_line,

-    

-    heatmap_width = unit(1, "npc"),

-    width = NULL,

-    heatmap_height = unit(1, "npc"),

-    height = NULL,

-    

-    show_heatmap_legend = TRUE,

-    heatmap_legend_param = list(title = name),

-    

-    use_raster = (nrow(matrix) > 2000 && ncol(matrix) > 1) || (ncol(matrix) > 2000 && nrow(matrix) > 1),

-    raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

-    raster_quality = 2,

-    raster_device_param = list(),

-    raster_resize = FALSE,

-    

-    post_fun = NULL)

-}

-\arguments{

-

-  \item{matrix}{A matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix.}

-  \item{col}{A vector of colors if the color mapping is discrete or a color mapping  function if the matrix is continuous numbers (should be generated by \code{\link[circlize]{colorRamp2}}). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated. Pass to \code{\link{ColorMapping}}. For more details and examples, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors} .}

-  \item{name}{Name of the heatmap. By default the heatmap name is used as the title of the heatmap legend.}

-  \item{na_col}{Color for \code{NA} values.}

-  \item{rect_gp}{Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by \code{\link[grid]{gpar}} and \code{fill} parameter is ignored.}

-  \item{color_space}{The color space in which colors are interpolated. Only used if \code{matrix} is numeric and  \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{border}{Whether draw border. The value can be logical or a string of color.}

-  \item{cell_fun}{Self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{j}, \code{i}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are column index, row index in \code{matrix}, coordinate of the cell, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

-  \item{layer_fun}{Similar as \code{cell_fun}, but is vectorized. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body} .}

-  \item{jitter}{Random shifts added to the matrix. The value can be logical or a single numeric value. It it is \code{TRUE}, random  values from uniform distribution between 0 and 1e-10 are generated. If it is a numeric value, the range for the uniform distribution is (0, \code{jitter}). It is mainly to solve the problem of "Error: node stack overflow" when there are too many identical rows/columns for plotting the dendrograms.}

-  \item{row_title}{Title on the row.}

-  \item{row_title_side}{Will the title be put on the left or right of the heatmap?}

-  \item{row_title_gp}{Graphic parameters for row title.}

-  \item{row_title_rot}{Rotation of row title. Only 0, 90, 270 are allowed to set.}

-  \item{column_title}{Title on the column.}

-  \item{column_title_side}{Will the title be put on the top or bottom of the heatmap?}

-  \item{column_title_gp}{Graphic parameters for column title.}

-  \item{column_title_rot}{Rotation of column titles. Only 0, 90, 270 are allowed to set.}

-  \item{cluster_rows}{If the value is a logical, it controls whether to make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} which already contains clustering. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering} .}

-  \item{cluster_row_slices}{If rows are split into slices, whether perform clustering on the slice means?}

-  \item{clustering_distance_rows}{It can be a pre-defined character which is in  ("euclidean", "maximum", "manhattan", "canberra", "binary",  "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and  the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors.}

-  \item{clustering_method_rows}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

-  \item{row_dend_side}{Should the row dendrogram be put on the left or right of the heatmap?}

-  \item{row_dend_width}{Width of the row dendrogram, should be a \code{\link[grid]{unit}} object.}

-  \item{show_row_dend}{Whether show row dendrogram?}

-  \item{row_dend_gp}{Graphic parameters for the dendrogram segments. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

-  \item{row_dend_reorder}{Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight  which is used to reorder rows. The reordering is applied by \code{\link[stats]{reorder.dendrogram}}.}

-  \item{cluster_columns}{Whether make cluster on columns? Same settings as \code{cluster_rows}.}

-  \item{cluster_column_slices}{If columns are split into slices, whether perform clustering on the slice means?}

-  \item{clustering_distance_columns}{Same setting as \code{clustering_distance_rows}.}

-  \item{clustering_method_columns}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

-  \item{column_dend_side}{Should the column dendrogram be put on the top or bottom of the heatmap?}

-  \item{column_dend_height}{height of the column cluster, should be a \code{\link[grid]{unit}} object.}

-  \item{show_column_dend}{Whether show column dendrogram?}

-  \item{column_dend_gp}{Graphic parameters for dendrogram segments. Same settings as \code{row_dend_gp}.}

-  \item{column_dend_reorder}{Apply reordering on column dendrograms. Same settings as \code{row_dend_reorder}.}

-  \item{row_order}{Order of rows. Manually setting row order turns off clustering.}

-  \item{column_order}{Order of column.}

-  \item{row_labels}{Optional row labels which are put as row names in the heatmap.}

-  \item{row_names_side}{Should the row names be put on the left or right of the heatmap?}

-  \item{show_row_names}{Whether show row names.}

-  \item{row_names_max_width}{Maximum width of row names viewport.}

-  \item{row_names_gp}{Graphic parameters for row names.}

-  \item{row_names_rot}{Rotation of row names.}

-  \item{row_names_centered}{Should row names put centered?}

-  \item{column_labels}{Optional column labels which are put as column names in the heatmap.}

-  \item{column_names_side}{Should the column names be put on the top or bottom of the heatmap?}

-  \item{column_names_max_height}{Maximum height of column names viewport.}

-  \item{show_column_names}{Whether show column names.}

-  \item{column_names_gp}{Graphic parameters for drawing text.}

-  \item{column_names_rot}{Rotation of column names.}

-  \item{column_names_centered}{Should column names put centered?}

-  \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object.}

-  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation}} object.}

-  \item{left_annotation}{It should be specified by \code{\link{rowAnnotation}}.}

-  \item{right_annotation}{it should be specified by \code{\link{rowAnnotation}}.}

-  \item{km}{Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above.}

-  \item{split}{A vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating to split the dendrogram by \code{\link[stats]{cutree}}.}

-  \item{row_km}{Same as \code{km}.}

-  \item{row_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Note if \code{row_km_repeats} is set to more than one, the final number of groups might be smaller than \code{row_km}, but this might means the original \code{row_km} is not a good choice.}

-  \item{row_split}{Same as \code{split}.}

-  \item{column_km}{K-means clustering on columns.}

-  \item{column_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Similar as \code{row_km_repeats}.}

-  \item{column_split}{Split on columns. For heatmap splitting, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split} .}

-  \item{gap}{Gap between row slices if the heatmap is split by rows. The value should be a \code{\link[grid]{unit}} object.}

-  \item{row_gap}{Same as \code{gap}.}

-  \item{column_gap}{Gap between column slices.}

-  \item{show_parent_dend_line}{When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?}

-  \item{width}{Width of the heatmap body.}

-  \item{height}{Height of the heatmap body.}

-  \item{heatmap_width}{Width of the whole heatmap (including heatmap components)}

-  \item{heatmap_height}{Height of the whole heatmap (including heatmap components). Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap} .}

-  \item{show_heatmap_legend}{Whether show heatmap legend?}

-  \item{heatmap_legend_param}{A list contains parameters for the heatmap legends. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

-  \item{use_raster}{Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

-  \item{raster_device}{Graphic device which is used to generate the raster image.}

-  \item{raster_quality}{A value set to larger than 1 will improve the quality of the raster image.}

-  \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

-  \item{raster_resize}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image?}

-  \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

-

-}

-\details{

-The initialization function only applies parameter checking and fill values to the slots with some validation.

-

-Following methods can be applied to the \code{\link{Heatmap-class}} object:

-

-\itemize{

-  \item \code{\link{show,Heatmap-method}}: draw a single heatmap with default parameters

-  \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.

-  \item \code{+} or \code{\link[=pct_v_pct]{\%v\%}} append heatmaps and annotations to a list of heatmaps.

-}

-

-The constructor function pretends to be a high-level graphic function because the \code{show} method

-of the \code{\link{Heatmap-class}} object actually plots the graphics.

-}

-\seealso{

-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html}

-}

-\value{

-A \code{\link{Heatmap-class}} object.

-}

-\author{

-Zuguang Gu <z.gu@dkfz.de>

-}

-\examples{

-# There is no example

-NULL

-

-}

@@ -14,6 +14,7 @@ Heatmap(matrix, col, name,

     border = NA,

     cell_fun = NULL,

     layer_fun = NULL,

+    jitter = FALSE,

     row_title = character(0),

     row_title_side = c("left", "right"),

@@ -106,6 +107,7 @@ Heatmap(matrix, col, name,

   \item{border}{Whether draw border. The value can be logical or a string of color.}

   \item{cell_fun}{Self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{j}, \code{i}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are column index, row index in \code{matrix}, coordinate of the cell, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

   \item{layer_fun}{Similar as \code{cell_fun}, but is vectorized. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body} .}

+  \item{jitter}{Random shifts added to the matrix. The value can be logical or a single numeric value. It it is \code{TRUE}, random  values from uniform distribution between 0 and 1e-10 are generated. If it is a numeric value, the range for the uniform distribution is (0, \code{jitter}). It is mainly to solve the problem of "Error: node stack overflow" when there are too many identical rows/columns for plotting the dendrograms.}

   \item{row_title}{Title on the row.}

   \item{row_title_side}{Will the title be put on the left or right of the heatmap?}

   \item{row_title_gp}{Graphic parameters for row title.}

@@ -204,4 +206,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -204,5 +204,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -52,12 +52,14 @@ Heatmap(matrix, col, name,

     row_names_max_width = unit(6, "cm"),

     row_names_gp = gpar(fontsize = 12),

     row_names_rot = 0,

+    row_names_centered = FALSE,

     column_labels = colnames(matrix),

     column_names_side = c("bottom", "top"),

     show_column_names = TRUE,

     column_names_max_height = unit(6, "cm"),

     column_names_gp = gpar(fontsize = 12),

     column_names_rot = 90,

+    column_names_centered = FALSE,

     top_annotation = NULL,

     bottom_annotation = NULL,

@@ -67,10 +69,10 @@ Heatmap(matrix, col, name,

     km = 1,

     split = NULL,

     row_km = km,

-    row_km_repeats = 10,

+    row_km_repeats = 1,

     row_split = split,

     column_km = 1,

-    column_km_repeats = 10,

+    column_km_repeats = 1,

     column_split = NULL,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

@@ -138,12 +140,14 @@ Heatmap(matrix, col, name,

   \item{row_names_max_width}{Maximum width of row names viewport.}

   \item{row_names_gp}{Graphic parameters for row names.}

   \item{row_names_rot}{Rotation of row names.}

+  \item{row_names_centered}{Should row names put centered?}

   \item{column_labels}{Optional column labels which are put as column names in the heatmap.}

   \item{column_names_side}{Should the column names be put on the top or bottom of the heatmap?}

   \item{column_names_max_height}{Maximum height of column names viewport.}

   \item{show_column_names}{Whether show column names.}

   \item{column_names_gp}{Graphic parameters for drawing text.}

   \item{column_names_rot}{Rotation of column names.}

+  \item{column_names_centered}{Should column names put centered?}

   \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object.}

   \item{bottom_annotation}{A \code{\link{HeatmapAnnotation}} object.}

   \item{left_annotation}{It should be specified by \code{\link{rowAnnotation}}.}

@@ -67,8 +67,10 @@ Heatmap(matrix, col, name,

     km = 1,

     split = NULL,

     row_km = km,

+    row_km_repeats = 10,

     row_split = split,

     column_km = 1,

+    column_km_repeats = 10,

     column_split = NULL,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

@@ -149,8 +151,10 @@ Heatmap(matrix, col, name,

   \item{km}{Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above.}

   \item{split}{A vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating to split the dendrogram by \code{\link[stats]{cutree}}.}

   \item{row_km}{Same as \code{km}.}

+  \item{row_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Note if \code{row_km_repeats} is set to more than one, the final number of groups might be smaller than \code{row_km}, but this might means the original \code{row_km} is not a good choice.}

   \item{row_split}{Same as \code{split}.}

   \item{column_km}{K-means clustering on columns.}

+  \item{column_km_repeats}{Number of k-means runs to get a consensus k-means clustering. Similar as \code{row_km_repeats}.}

   \item{column_split}{Split on columns. For heatmap splitting, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split} .}

   \item{gap}{Gap between row slices if the heatmap is split by rows. The value should be a \code{\link[grid]{unit}} object.}

   \item{row_gap}{Same as \code{gap}.}

@@ -196,4 +196,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -196,5 +196,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -25,6 +25,7 @@ Heatmap(matrix, col, name,

     column_title_rot = 0,

     cluster_rows = TRUE,

+    cluster_row_slices = TRUE,

     clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete",

     row_dend_side = c("left", "right"),

@@ -33,6 +34,7 @@ Heatmap(matrix, col, name,

     row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

     row_dend_gp = gpar(),

     cluster_columns = TRUE,

+    cluster_column_slices = TRUE,

     clustering_distance_columns = "euclidean",

     clustering_method_columns = "complete",

     column_dend_side = c("top", "bottom"),

@@ -85,6 +87,7 @@ Heatmap(matrix, col, name,

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

     raster_device_param = list(),

+    raster_resize = FALSE,

     post_fun = NULL)

 }

@@ -108,6 +111,7 @@ Heatmap(matrix, col, name,

   \item{column_title_gp}{Graphic parameters for column title.}

   \item{column_title_rot}{Rotation of column titles. Only 0, 90, 270 are allowed to set.}

   \item{cluster_rows}{If the value is a logical, it controls whether to make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} which already contains clustering. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering} .}

+  \item{cluster_row_slices}{If rows are split into slices, whether perform clustering on the slice means?}

   \item{clustering_distance_rows}{It can be a pre-defined character which is in  ("euclidean", "maximum", "manhattan", "canberra", "binary",  "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and  the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors.}

   \item{clustering_method_rows}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

   \item{row_dend_side}{Should the row dendrogram be put on the left or right of the heatmap?}

@@ -116,6 +120,7 @@ Heatmap(matrix, col, name,

   \item{row_dend_gp}{Graphic parameters for the dendrogram segments. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

   \item{row_dend_reorder}{Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight  which is used to reorder rows. The reordering is applied by \code{\link[stats]{reorder.dendrogram}}.}

   \item{cluster_columns}{Whether make cluster on columns? Same settings as \code{cluster_rows}.}

+  \item{cluster_column_slices}{If columns are split into slices, whether perform clustering on the slice means?}

   \item{clustering_distance_columns}{Same setting as \code{clustering_distance_rows}.}

   \item{clustering_method_columns}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

   \item{column_dend_side}{Should the column dendrogram be put on the top or bottom of the heatmap?}

@@ -161,6 +166,7 @@ Heatmap(matrix, col, name,

   \item{raster_device}{Graphic device which is used to generate the raster image.}

   \item{raster_quality}{A value set to larger than 1 will improve the quality of the raster image.}

   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

+  \item{raster_resize}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image?}

   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

 }

@@ -30,7 +30,7 @@ Heatmap(matrix, col, name,

     row_dend_side = c("left", "right"),

     row_dend_width = unit(10, "mm"),

     show_row_dend = TRUE,

-    row_dend_reorder = TRUE,

+    row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows),

     row_dend_gp = gpar(),

     cluster_columns = TRUE,

     clustering_distance_columns = "euclidean",

@@ -39,7 +39,7 @@ Heatmap(matrix, col, name,

     column_dend_height = unit(10, "mm"),

     show_column_dend = TRUE,

     column_dend_gp = gpar(),

-    column_dend_reorder = TRUE,

+    column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns),

     row_order = NULL,

     column_order = NULL,

@@ -71,6 +71,7 @@ Heatmap(matrix, col, name,

     gap = unit(1, "mm"),

     row_gap = unit(1, "mm"),

     column_gap = unit(1, "mm"),

+    show_parent_dend_line = ht_opt$show_parent_dend_line,

     heatmap_width = unit(1, "npc"),

     width = NULL,

@@ -149,6 +150,7 @@ Heatmap(matrix, col, name,

   \item{gap}{Gap between row slices if the heatmap is split by rows. The value should be a \code{\link[grid]{unit}} object.}

   \item{row_gap}{Same as \code{gap}.}

   \item{column_gap}{Gap between column slices.}

+  \item{show_parent_dend_line}{When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?}

   \item{width}{Width of the heatmap body.}

   \item{height}{Height of the heatmap body.}

   \item{heatmap_width}{Width of the whole heatmap (including heatmap components)}

@@ -89,93 +89,96 @@ Heatmap(matrix, col, name,

 }

 \arguments{

-  \item{matrix}{a matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix.}

-  \item{col}{a vector of colors if the color mapping is discrete or a color mapping  function if the matrix is continuous numbers (should be generated by \code{\link[circlize]{colorRamp2}}. If the matrix is continuous, the value can also be a vector of colors so that colors will be interpolated. Pass to \code{\link{ColorMapping}}.}

-  \item{name}{name of the heatmap. The name is used as the title of the heatmap legend.}

-  \item{na_col}{color for \code{NA} values.}

-  \item{rect_gp}{graphic parameters for drawing rectangles (for heatmap body).}

-  \item{color_space}{the color space in which colors are interpolated. Only used if \code{matrix} is numeric and  \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{border}{whether draw border or the color of border.}

-  \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index, column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

-  \item{layer_fun}{similar as \code{cell_fun}, but is vectorized. }

-  \item{row_title}{title on row.}

-  \item{row_title_side}{will the title be put on the left or right of the heatmap?}

-  \item{row_title_gp}{graphic parameters for drawing text.}

-  \item{row_title_rot}{rotation of row titles. Only 0, 90, 270 are allowed to set.}

-  \item{column_title}{title on column.}

-  \item{column_title_side}{will the title be put on the top or bottom of the heatmap?}

-  \item{column_title_gp}{graphic parameters for drawing text.}

-  \item{column_title_rot}{rotation of column titles. Only 0, 90, 270 are allowed to set.}

-  \item{cluster_rows}{If the value is a logical, it means whether make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} that already contains clustering information. This means you can use any type of clustering methods and render the \code{\link[stats]{dendrogram}} object with self-defined graphic settings.}

-  \item{clustering_distance_rows}{it can be a pre-defined character which is in  ("euclidean", "maximum", "manhattan", "canberra", "binary",  "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and  the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors.}

-  \item{clustering_method_rows}{method to make cluster, pass to \code{\link[stats]{hclust}}.}

-  \item{row_dend_side}{should the row cluster be put on the left or right of the heatmap?}

-  \item{row_dend_width}{width of the row cluster, should be a \code{\link[grid]{unit}} object.}

-  \item{show_row_dend}{whether show row clusters. }

-  \item{row_dend_gp}{graphics parameters for drawing lines. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

-  \item{row_dend_reorder}{apply reordering on rows. The value can be a logical value or a vector which contains weight  which is used to reorder rows}

-  \item{cluster_columns}{whether make cluster on columns. Same settings as \code{cluster_rows}.}

-  \item{clustering_distance_columns}{same setting as \code{clustering_distance_rows}.}

-  \item{clustering_method_columns}{method to make cluster, pass to \code{\link[stats]{hclust}}.}

-  \item{column_dend_side}{should the column cluster be put on the top or bottom of the heatmap?}

+  \item{matrix}{A matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix.}

+  \item{col}{A vector of colors if the color mapping is discrete or a color mapping  function if the matrix is continuous numbers (should be generated by \code{\link[circlize]{colorRamp2}}). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated. Pass to \code{\link{ColorMapping}}. For more details and examples, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors} .}

+  \item{name}{Name of the heatmap. By default the heatmap name is used as the title of the heatmap legend.}

+  \item{na_col}{Color for \code{NA} values.}

+  \item{rect_gp}{Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by \code{\link[grid]{gpar}} and \code{fill} parameter is ignored.}

+  \item{color_space}{The color space in which colors are interpolated. Only used if \code{matrix} is numeric and  \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}

+  \item{border}{Whether draw border. The value can be logical or a string of color.}

+  \item{cell_fun}{Self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{j}, \code{i}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are column index, row index in \code{matrix}, coordinate of the cell, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

+  \item{layer_fun}{Similar as \code{cell_fun}, but is vectorized. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body} .}

+  \item{row_title}{Title on the row.}

+  \item{row_title_side}{Will the title be put on the left or right of the heatmap?}

+  \item{row_title_gp}{Graphic parameters for row title.}

+  \item{row_title_rot}{Rotation of row title. Only 0, 90, 270 are allowed to set.}

+  \item{column_title}{Title on the column.}

+  \item{column_title_side}{Will the title be put on the top or bottom of the heatmap?}

+  \item{column_title_gp}{Graphic parameters for column title.}

+  \item{column_title_rot}{Rotation of column titles. Only 0, 90, 270 are allowed to set.}

+  \item{cluster_rows}{If the value is a logical, it controls whether to make cluster on rows. The value can also be a \code{\link[stats]{hclust}} or a \code{\link[stats]{dendrogram}} which already contains clustering. Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering} .}

+  \item{clustering_distance_rows}{It can be a pre-defined character which is in  ("euclidean", "maximum", "manhattan", "canberra", "binary",  "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and  the returned value should be a \code{\link[stats]{dist}} object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors.}

+  \item{clustering_method_rows}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

+  \item{row_dend_side}{Should the row dendrogram be put on the left or right of the heatmap?}

+  \item{row_dend_width}{Width of the row dendrogram, should be a \code{\link[grid]{unit}} object.}

+  \item{show_row_dend}{Whether show row dendrogram?}

+  \item{row_dend_gp}{Graphic parameters for the dendrogram segments. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

+  \item{row_dend_reorder}{Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight  which is used to reorder rows. The reordering is applied by \code{\link[stats]{reorder.dendrogram}}.}

+  \item{cluster_columns}{Whether make cluster on columns? Same settings as \code{cluster_rows}.}

+  \item{clustering_distance_columns}{Same setting as \code{clustering_distance_rows}.}

+  \item{clustering_method_columns}{Method to perform hierarchical clustering, pass to \code{\link[stats]{hclust}}.}

+  \item{column_dend_side}{Should the column dendrogram be put on the top or bottom of the heatmap?}

   \item{column_dend_height}{height of the column cluster, should be a \code{\link[grid]{unit}} object.}

-  \item{show_column_dend}{whether show column clusters.}

-  \item{column_dend_gp}{graphic parameters for drawling lines. Same settings as \code{row_dend_gp}.}

-  \item{column_dend_reorder}{apply reordering on columns. The value can be a logical value or a vector which contains weight  which is used to reorder columns}

-  \item{row_order}{order of rows. It makes it easy to adjust row order for a list of heatmaps if this heatmap  is selected as the main heatmap. Manually setting row order should turn off clustering}

-  \item{column_order}{order of column. It makes it easy to adjust column order for both matrix and column annotations.}

-  \item{row_labels}{row labels}

-  \item{row_names_side}{should the row names be put on the left or right of the heatmap?}

-  \item{show_row_names}{whether show row names.}

-  \item{row_names_max_width}{maximum width of row names viewport. Because some times row names can be very long, it is not reasonable to show them all.}

-  \item{row_names_gp}{graphic parameters for drawing text.}

-  \item{row_names_rot}{rotation of row labels}

-  \item{column_labels}{column labels}

-  \item{column_names_side}{should the column names be put on the top or bottom of the heatmap?}

-  \item{column_names_max_height}{maximum height of column names viewport.}

-  \item{show_column_names}{whether show column names.}

-  \item{column_names_gp}{graphic parameters for drawing text.}

-  \item{column_names_rot}{rotation of column labels}

-  \item{top_annotation}{a \code{\link{HeatmapAnnotation}} object which contains a list of annotations.}

-  \item{bottom_annotation}{a \code{\link{HeatmapAnnotation}} object.}

-  \item{left_annotation}{should specified in \code{\link{rowAnnotation}}}

-  \item{right_annotation}{should shpecified in \code{\link{rowAnnotation}}}

-  \item{km}{do k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row-clusters, hierarchical clustering is still applied with parameters above.}

-  \item{split}{a vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating rows are to be split according to the split on the tree.}

-  \item{row_km}{row km}

-  \item{row_split}{row split}

-  \item{column_km}{column km}

-  \item{column_split}{column split}

-  \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object. If it is a vector, the order corresponds to top to bottom in the heatmap}

-  \item{row_gap}{row gap}

-  \item{column_gap}{column gap}

-  \item{width}{width of the heatmap body}

-  \item{height}{height of the heatmap body}

-  \item{heatmap_width}{width of the whole heatmap (including heatmap components)}

-  \item{heatmap_height}{height of the whole heatmap (including heatmap components)}

-  \item{show_heatmap_legend}{whether show heatmap legend?}

-  \item{heatmap_legend_param}{a list contains parameters for the heatmap legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

-  \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

-  \item{raster_device}{graphic device which is used to generate the raster image}

-  \item{raster_quality}{a value set to larger than 1 will improve the quality of the raster image.}

-  \item{raster_device_param}{a list of further parameters for the selected graphic device}

-  \item{post_fun}{a function which will be executed after the plot is drawn.}

+  \item{show_column_dend}{Whether show column dendrogram?}

+  \item{column_dend_gp}{Graphic parameters for dendrogram segments. Same settings as \code{row_dend_gp}.}

+  \item{column_dend_reorder}{Apply reordering on column dendrograms. Same settings as \code{row_dend_reorder}.}

+  \item{row_order}{Order of rows. Manually setting row order turns off clustering.}

+  \item{column_order}{Order of column.}

+  \item{row_labels}{Optional row labels which are put as row names in the heatmap.}

+  \item{row_names_side}{Should the row names be put on the left or right of the heatmap?}

+  \item{show_row_names}{Whether show row names.}

+  \item{row_names_max_width}{Maximum width of row names viewport.}

+  \item{row_names_gp}{Graphic parameters for row names.}

+  \item{row_names_rot}{Rotation of row names.}

+  \item{column_labels}{Optional column labels which are put as column names in the heatmap.}

+  \item{column_names_side}{Should the column names be put on the top or bottom of the heatmap?}

+  \item{column_names_max_height}{Maximum height of column names viewport.}

+  \item{show_column_names}{Whether show column names.}

+  \item{column_names_gp}{Graphic parameters for drawing text.}

+  \item{column_names_rot}{Rotation of column names.}

+  \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object.}

+  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation}} object.}

+  \item{left_annotation}{It should be specified by \code{\link{rowAnnotation}}.}

+  \item{right_annotation}{it should be specified by \code{\link{rowAnnotation}}.}

+  \item{km}{Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above.}

+  \item{split}{A vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating to split the dendrogram by \code{\link[stats]{cutree}}.}

+  \item{row_km}{Same as \code{km}.}

+  \item{row_split}{Same as \code{split}.}

+  \item{column_km}{K-means clustering on columns.}

+  \item{column_split}{Split on columns. For heatmap splitting, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split} .}

+  \item{gap}{Gap between row slices if the heatmap is split by rows. The value should be a \code{\link[grid]{unit}} object.}

+  \item{row_gap}{Same as \code{gap}.}

+  \item{column_gap}{Gap between column slices.}

+  \item{width}{Width of the heatmap body.}

+  \item{height}{Height of the heatmap body.}

+  \item{heatmap_width}{Width of the whole heatmap (including heatmap components)}

+  \item{heatmap_height}{Height of the whole heatmap (including heatmap components). Check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap} .}

+  \item{show_heatmap_legend}{Whether show heatmap legend?}

+  \item{heatmap_legend_param}{A list contains parameters for the heatmap legends. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

+  \item{use_raster}{Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

+  \item{raster_device}{Graphic device which is used to generate the raster image.}

+  \item{raster_quality}{A value set to larger than 1 will improve the quality of the raster image.}

+  \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

+  \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

 }

 \details{

-The initialization function only applies parameter checking and fill values to the slots with proper values.

+The initialization function only applies parameter checking and fill values to the slots with some validation.

-Following methods can be applied on the \code{\link{Heatmap-class}} object:

+Following methods can be applied to the \code{\link{Heatmap-class}} object:

 \itemize{

   \item \code{\link{show,Heatmap-method}}: draw a single heatmap with default parameters

   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.

-  \item \code{+} or \code{\link[=pct_v_pct]{\%v\%}} append heatmaps and row annotations to a list of heatmaps.

+  \item \code{+} or \code{\link[=pct_v_pct]{\%v\%}} append heatmaps and annotations to a list of heatmaps.

 }

 The constructor function pretends to be a high-level graphic function because the \code{show} method

 of the \code{\link{Heatmap-class}} object actually plots the graphics.

 }

+\seealso{

+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html}

+}

 \value{

 A \code{\link{Heatmap-class}} object.

 }

@@ -185,4 +185,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -185,5 +185,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -80,7 +80,7 @@ Heatmap(matrix, col, name,

     show_heatmap_legend = TRUE,

     heatmap_legend_param = list(title = name),

-    use_raster = nrow(matrix) > 2000 || ncol(matrix) > 2000,

+    use_raster = (nrow(matrix) > 2000 && ncol(matrix) > 1) || (ncol(matrix) > 2000 && nrow(matrix) > 1),

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

     raster_device_param = list(),

@@ -185,4 +185,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

@@ -68,19 +68,19 @@ Heatmap(matrix, col, name,

     row_split = split,

     column_km = 1,

     column_split = NULL,

-    gap = unit(0.5, "mm"),

-    row_gap = unit(0.5, "mm"),

-    column_gap = unit(0.5, "mm"),

+    gap = unit(1, "mm"),

+    row_gap = unit(1, "mm"),

+    column_gap = unit(1, "mm"),

-    width = unit(1, "npc"),

-    heatmap_body_width = NULL,

-    height = unit(1, "npc"),

-    heatmap_body_height = NULL,

+    heatmap_width = unit(1, "npc"),

+    width = NULL,

+    heatmap_height = unit(1, "npc"),

+    height = NULL,

     show_heatmap_legend = TRUE,

     heatmap_legend_param = list(title = name),

-    use_raster = nrow(matrix) > 5000,

+    use_raster = nrow(matrix) > 2000 || ncol(matrix) > 2000,

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

     raster_device_param = list(),

@@ -95,9 +95,9 @@ Heatmap(matrix, col, name,

   \item{na_col}{color for \code{NA} values.}

   \item{rect_gp}{graphic parameters for drawing rectangles (for heatmap body).}

   \item{color_space}{the color space in which colors are interpolated. Only used if \code{matrix} is numeric and  \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{border}{border}

+  \item{border}{whether draw border or the color of border.}

   \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index, column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

-  \item{layer_fun}{layer fun}

+  \item{layer_fun}{similar as \code{cell_fun}, but is vectorized. }

   \item{row_title}{title on row.}

   \item{row_title_side}{will the title be put on the left or right of the heatmap?}

   \item{row_title_gp}{graphic parameters for drawing text.}

@@ -149,10 +149,10 @@ Heatmap(matrix, col, name,

   \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object. If it is a vector, the order corresponds to top to bottom in the heatmap}

   \item{row_gap}{row gap}

   \item{column_gap}{column gap}

-  \item{width}{width}

-  \item{height}{height}

-  \item{heatmap_body_width}{width}

-  \item{heatmap_body_height}{height}

+  \item{width}{width of the heatmap body}

+  \item{height}{height of the heatmap body}

+  \item{heatmap_width}{width of the whole heatmap (including heatmap components)}

+  \item{heatmap_height}{height of the whole heatmap (including heatmap components)}

   \item{show_heatmap_legend}{whether show heatmap legend?}

   \item{heatmap_legend_param}{a list contains parameters for the heatmap legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

   \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

@@ -163,15 +163,14 @@ Heatmap(matrix, col, name,

 }

 \details{

-The initialization function only applies parameter checking and fill values to each slot with proper ones.

-Then it will be ready for clustering and layout.

+The initialization function only applies parameter checking and fill values to the slots with proper values.

 Following methods can be applied on the \code{\link{Heatmap-class}} object:

 \itemize{

   \item \code{\link{show,Heatmap-method}}: draw a single heatmap with default parameters

   \item \code{\link{draw,Heatmap-method}}: draw a single heatmap.

-  \item \code{\link{add_heatmap,Heatmap-method}} append heatmaps and row annotations to a list of heatmaps.

+  \item \code{+} or \code{\link[=pct_v_pct]{\%v\%}} append heatmaps and row annotations to a list of heatmaps.

 }

 The constructor function pretends to be a high-level graphic function because the \code{show} method

@@ -186,5 +185,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -186,4 +186,5 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

+

 }

old mode 100755

new mode 100644

@@ -11,7 +11,10 @@ Heatmap(matrix, col, name,

     na_col = "grey",

     color_space = "LAB",

     rect_gp = gpar(col = NA),

+    border = NA,

     cell_fun = NULL,

+    layer_fun = NULL,

+    

     row_title = character(0),

     row_title_side = c("left", "right"),

     row_title_gp = gpar(fontsize = 14),

@@ -20,6 +23,7 @@ Heatmap(matrix, col, name,

     column_title_side = c("top", "bottom"),

     column_title_gp = gpar(fontsize = 14),

     column_title_rot = 0,

+    

     cluster_rows = TRUE,

     clustering_distance_rows = "euclidean",

     clustering_method_rows = "complete",

@@ -28,11 +32,6 @@ Heatmap(matrix, col, name,

     show_row_dend = TRUE,

     row_dend_reorder = TRUE,

     row_dend_gp = gpar(),

-    row_hclust_side = row_dend_side,

-    row_hclust_width = row_dend_width,

-    show_row_hclust = show_row_dend,

-    row_hclust_reorder = row_dend_reorder,

-    row_hclust_gp = row_dend_gp,

     cluster_columns = TRUE,

     clustering_distance_columns = "euclidean",

     clustering_method_columns = "complete",

@@ -41,37 +40,52 @@ Heatmap(matrix, col, name,

     show_column_dend = TRUE,

     column_dend_gp = gpar(),

     column_dend_reorder = TRUE,

-    column_hclust_side = column_dend_side,

-    column_hclust_height = column_dend_height,

-    show_column_hclust = show_column_dend,

-    column_hclust_gp = column_dend_gp,

-    column_hclust_reorder = column_dend_reorder,

+    

     row_order = NULL,

     column_order = NULL,

+    

+    row_labels = rownames(matrix),

     row_names_side = c("right", "left"),

     show_row_names = TRUE,

-    row_names_max_width = default_row_names_max_width(),

+    row_names_max_width = unit(6, "cm"),

     row_names_gp = gpar(fontsize = 12),

+    row_names_rot = 0,

+    column_labels = colnames(matrix),

     column_names_side = c("bottom", "top"),

     show_column_names = TRUE,

-    column_names_max_height = default_column_names_max_height(),

+    column_names_max_height = unit(6, "cm"),

     column_names_gp = gpar(fontsize = 12),

-    top_annotation = new("HeatmapAnnotation"),

-    top_annotation_height = top_annotation@size,

-    bottom_annotation = new("HeatmapAnnotation"),

-    bottom_annotation_height = bottom_annotation@size,

+    column_names_rot = 90,

+    

+    top_annotation = NULL,

+    bottom_annotation = NULL,

+    left_annotation = NULL,

+    right_annotation = NULL,

+    

     km = 1,

-    km_title = "cluster\%i",

     split = NULL,

-    gap = unit(1, "mm"),

-    combined_name_fun = function(x) paste(x, collapse = "/"),

-    width = NULL,

+    row_km = km,

+    row_split = split,

+    column_km = 1,

+    column_split = NULL,

+    gap = unit(0.5, "mm"),

+    row_gap = unit(0.5, "mm"),

+    column_gap = unit(0.5, "mm"),

+    

+    width = unit(1, "npc"),

+    heatmap_body_width = NULL,

+    height = unit(1, "npc"),

+    heatmap_body_height = NULL,

+    

     show_heatmap_legend = TRUE,

     heatmap_legend_param = list(title = name),

-    use_raster = FALSE,

+    

+    use_raster = nrow(matrix) > 5000,

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

     raster_quality = 2,

-    raster_device_param = list())

+    raster_device_param = list(),

+    

+    post_fun = NULL)

 }

 \arguments{

@@ -81,7 +95,9 @@ Heatmap(matrix, col, name,

   \item{na_col}{color for \code{NA} values.}

   \item{rect_gp}{graphic parameters for drawing rectangles (for heatmap body).}

   \item{color_space}{the color space in which colors are interpolated. Only used if \code{matrix} is numeric and  \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}

+  \item{border}{border}

   \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into  this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index, column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport, the width and height of the cell and the filled color. \code{x}, \code{y}, \code{width} and \code{height} are all \code{\link[grid]{unit}} objects.}

+  \item{layer_fun}{layer fun}

   \item{row_title}{title on row.}

   \item{row_title_side}{will the title be put on the left or right of the heatmap?}

   \item{row_title_gp}{graphic parameters for drawing text.}

@@ -98,11 +114,6 @@ Heatmap(matrix, col, name,

   \item{show_row_dend}{whether show row clusters. }

   \item{row_dend_gp}{graphics parameters for drawing lines. If users already provide a \code{\link[stats]{dendrogram}} object with edges rendered, this argument will be ignored.}

   \item{row_dend_reorder}{apply reordering on rows. The value can be a logical value or a vector which contains weight  which is used to reorder rows}

-  \item{row_hclust_side}{deprecated, use \code{row_dend_side} instead}

-  \item{row_hclust_width}{deprecated, use \code{row_dend_width} instead}

-  \item{show_row_hclust}{deprecated, use \code{show_row_dend} instead}

-  \item{row_hclust_gp}{deprecated, use \code{row_dend_gp} instead}

-  \item{row_hclust_reorder}{deprecated, use \code{row_dend_reorder} instead}

   \item{cluster_columns}{whether make cluster on columns. Same settings as \code{cluster_rows}.}

   \item{clustering_distance_columns}{same setting as \code{clustering_distance_rows}.}

   \item{clustering_method_columns}{method to make cluster, pass to \code{\link[stats]{hclust}}.}

@@ -111,37 +122,44 @@ Heatmap(matrix, col, name,

   \item{show_column_dend}{whether show column clusters.}

   \item{column_dend_gp}{graphic parameters for drawling lines. Same settings as \code{row_dend_gp}.}

   \item{column_dend_reorder}{apply reordering on columns. The value can be a logical value or a vector which contains weight  which is used to reorder columns}

-  \item{column_hclust_side}{deprecated, use \code{column_dend_side} instead}

-  \item{column_hclust_height}{deprecated, use \code{column_dend_height} instead}

-  \item{show_column_hclust}{deprecated, use \code{show_column_dend} instead}

-  \item{column_hclust_gp}{deprecated, use \code{column_dend_gp} instead}

-  \item{column_hclust_reorder}{deprecated, use \code{column_dend_reorder} instead}

   \item{row_order}{order of rows. It makes it easy to adjust row order for a list of heatmaps if this heatmap  is selected as the main heatmap. Manually setting row order should turn off clustering}

   \item{column_order}{order of column. It makes it easy to adjust column order for both matrix and column annotations.}

+  \item{row_labels}{row labels}

   \item{row_names_side}{should the row names be put on the left or right of the heatmap?}

   \item{show_row_names}{whether show row names.}

   \item{row_names_max_width}{maximum width of row names viewport. Because some times row names can be very long, it is not reasonable to show them all.}

   \item{row_names_gp}{graphic parameters for drawing text.}

+  \item{row_names_rot}{rotation of row labels}

+  \item{column_labels}{column labels}

   \item{column_names_side}{should the column names be put on the top or bottom of the heatmap?}

   \item{column_names_max_height}{maximum height of column names viewport.}

   \item{show_column_names}{whether show column names.}

   \item{column_names_gp}{graphic parameters for drawing text.}

+  \item{column_names_rot}{rotation of column labels}

   \item{top_annotation}{a \code{\link{HeatmapAnnotation}} object which contains a list of annotations.}

-  \item{top_annotation_height}{total height of the column annotations on the top.}

   \item{bottom_annotation}{a \code{\link{HeatmapAnnotation}} object.}

-  \item{bottom_annotation_height}{total height of the column annotations on the bottom.}

+  \item{left_annotation}{should specified in \code{\link{rowAnnotation}}}

+  \item{right_annotation}{should shpecified in \code{\link{rowAnnotation}}}

   \item{km}{do k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row-clusters, hierarchical clustering is still applied with parameters above.}

-  \item{km_title}{row title for each cluster when \code{km} is set. It must a text with format of ".*\%i.*" where "\%i" is replaced by the index of the cluster.}

   \item{split}{a vector or a data frame by which the rows are split. But if \code{cluster_rows} is a clustering object, \code{split} can be a single number indicating rows are to be split according to the split on the tree.}

+  \item{row_km}{row km}

+  \item{row_split}{row split}

+  \item{column_km}{column km}

+  \item{column_split}{column split}

   \item{gap}{gap between row-slices if the heatmap is split by rows, should be \code{\link[grid]{unit}} object. If it is a vector, the order corresponds to top to bottom in the heatmap}

-  \item{combined_name_fun}{if the heatmap is split by rows, how to make a combined row title for each slice? The input parameter for this function is a vector which contains level names under each column in \code{split}.}

-  \item{width}{the width of the single heatmap, should be a fixed \code{\link[grid]{unit}} object. It is used for the layout when the heatmap is appended to a list of heatmaps.}

+  \item{row_gap}{row gap}

+  \item{column_gap}{column gap}

+  \item{width}{width}

+  \item{height}{height}

+  \item{heatmap_body_width}{width}

+  \item{heatmap_body_height}{height}

   \item{show_heatmap_legend}{whether show heatmap legend?}

   \item{heatmap_legend_param}{a list contains parameters for the heatmap legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}

   \item{use_raster}{whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}

   \item{raster_device}{graphic device which is used to generate the raster image}

   \item{raster_quality}{a value set to larger than 1 will improve the quality of the raster image.}