@@ -14,6 +14,7 @@ a color mapping function.

 }

 \section{Methods}{

 The \code{\link{ColorMapping-class}} provides following methods:

+

 \itemize{

   \item \code{\link{ColorMapping}}: contructor methods.

   \item \code{\link{map_to_colors,ColorMapping-method}}: mapping values to colors.

@@ -10,8 +10,10 @@ Making complex heatmap

 \details{

 This package aims to provide a simple and flexible way to arrange

 multiple heatmaps as well as self-defining annotation graphics.

+

 The package is implemented in an object-oriented way. 

 Components of heatmap lists are abstracted into several classes.

+

 \itemize{

   \item \code{\link{Heatmap-class}}: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.

   \item \code{\link{HeatmapList-class}}: a list of heatmaps and row annotations.

@@ -19,6 +21,7 @@ Components of heatmap lists are abstracted into several classes.

 }

 There are also several internal classes:

+

 \itemize{

   \item \code{\link{SingleAnnotation-class}}: a single row annotation or column annotation.

   \item \code{\link{ColorMapping-class}}: mapping from values to colors.

@@ -26,5 +29,6 @@ There are also several internal classes:

 For plotting one single heatmap, please go to the documentation page of \code{\link{Heatmap}}.

 For plotting multiple heatmaps, please go to \code{\link{HeatmapList-class}} and \code{+.AdditiveUnit}.

+

 The vignette provides detailed explanation of how to use this package.

 }

@@ -9,6 +9,7 @@ Class for a single heatmap

 }

 \details{

 The components for a single heamtap are placed into a 9 x 7 layout:

+

   \preformatted{

 +------+ (1)

          +------+ (2)

@@ -23,6 +24,7 @@ The components for a single heamtap are placed into a 9 x 7 layout:

          +------+ (9)  }

 From top to bottom in column 4, the regions are:

+

 \itemize{

   \item title which is put on the top of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

   \item column cluster on the top, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.

@@ -36,6 +38,7 @@ From top to bottom in column 4, the regions are:

 }

 From left to right in row 5, the regions are:

+

 \itemize{

   \item title which is put in the left of the heatmap, graphics are drawn by \code{\link{draw_title,Heatmap-method}}.

   \item row cluster on the left, graphics are drawn by \code{\link{draw_hclust,Heatmap-method}}.

@@ -52,6 +55,7 @@ and call \code{\link{draw,HeatmapList-method}} to make a complete heatmap.

 }

 \section{Methods}{

 The \code{\link{Heatmap-class}} provides following methods:

+

 \itemize{

   \item \code{\link{Heatmap}}: constructor method.

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

@@ -96,7 +96,9 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),

 \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.

+

 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.

@@ -14,6 +14,7 @@ represented as a list of \code{\link{SingleAnnotation-class}} objects with same

 }

 \section{Methods}{

 The \code{\link{HeatmapAnnotation-class}} provides following methods:

+

 \itemize{

   \item \code{\link{HeatmapAnnotation}}: constructor method

   \item \code{\link{draw,HeatmapAnnotation-method}}: draw the annotations

@@ -9,7 +9,9 @@ Class for a list of heatmaps

 }

 \details{

 A heatmap list is defined as a list of heatmaps and row annotations.

+

 The components for the heamtap list are placed into a 7 x 7 layout:

+

   \preformatted{

 +------+(1)

          +------+(2)

@@ -22,6 +24,7 @@ The components for the heamtap list are placed into a 7 x 7 layout:

          +------+(7)  }

 From top to bottom in column 4, the regions are:

+

 \itemize{

   \item annotation legend on the top, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

   \item heatmap legend on the top, graphics are drawn by \code{\link{draw_heatmap_legend,HeatmapList-method}}.

@@ -33,6 +36,7 @@ From top to bottom in column 4, the regions are:

 }

 From left to right in row 4, the regions are:

+

 \itemize{

   \item annotation legend on the left, graphics are drawn by \code{\link{draw_annotation_legend,HeatmapList-method}}.

   \item heatmap legend on the left, graphics are drawn by \code{\link{draw_heatmap_legend,HeatmapList-method}}.

@@ -48,6 +52,7 @@ are placed one after the other.

 }

 \section{Methods}{

 The \code{\link{HeatmapList-class}} provides following methods:

+

 \itemize{

   \item \code{\link{draw,HeatmapList-method}}: draw the list of heatmaps and row annotations.

   \item \code{\link{add_heatmap,HeatmapList-method}} add heatmaps to the list of heatmaps.

@@ -13,11 +13,13 @@ the \code{\link{SingleAnnotation-class}} defines the basic unit of annotations.

 The most simple annotation is one row or one column grids in which different colors

 represent different classes of the data. The annotation can also be more complex

 graphics, such as a boxplot that shows data distribution in corresponding row or column.

+

 The \code{\link{SingleAnnotation-class}} is used for storing data for a single annotation and provides

 methods for drawing annotation graphics.

 }

 \section{Methods}{

 The \code{\link{SingleAnnotation-class}} provides following methods:

+

 \itemize{

   \item \code{\link{SingleAnnotation}}: constructor method

   \item \code{\link{draw,SingleAnnotation-method}}: draw the single annotation.

@@ -27,12 +27,15 @@ The most simple annotation is one row or one column grids in which different col

 represent different classes of the data. Here the function use \code{\link{ColorMapping-class}}

 to process such simple annotation. \code{value} and \code{col} arguments controls values and colors

 of the simple annotation and a \code{\link{ColorMapping-class}} object will be constructed based on \code{value} and \code{col}.

+

 \code{fun} is used to construct a more complex annotation. Users can add any type of annotation graphics

 by implementing a function. The only input argument of \code{fun} is a index

 of rows or columns which is already adjusted by the clustering. In the package, there are already

 several annotation graphic function generators: \code{\link{anno_points}}, \code{\link{anno_histogram}} and \code{\link{anno_boxplot}}.

+

 In the case that row annotations are splitted by rows, \code{index} corresponding to row orders in each row-slice

 and \code{fun} will be applied on each of the row slices.

+

 One thing that users should be careful is the difference of coordinates when the annotation is a row

 annotation or a column annotation.

 }

@@ -18,6 +18,7 @@ Add heatmaps or row annotations to a heatmap list

 \details{

 It is only a shortcut function. It actually calls \code{\link{add_heatmap,Heatmap-method}}, \code{\link{add_heatmap,HeatmapList-method}}

 or \code{\link{add_heatmap,HeatmapAnnotation-method}} depending on the class of the input objects.

+

 The \code{\link{HeatmapAnnotation-class}} object to be added should only be row annotations.

 }

 \value{

@@ -20,6 +20,7 @@ Size of the annotation legend viewport

 \details{

 Legends for all heatmaps or legends for all annotations will be put in one viewport. This function

 calculates the size of such viewport. Note graphic parameters for legends will affect the size.

+

 This function is only for internal use.

 }

 \value{

@@ -40,6 +40,7 @@ Draw legend based on color mapping

 }

 \details{

 A viewport is created which contains a legend title, legend grids and corresponding labels.

+

 This function will be improved in the future to support more types of legends.

 }

 \value{

@@ -16,6 +16,7 @@ columnAnnotation(...)

 }

 \details{

 The function is identical to

+

   \preformatted{

 HeatmapAnnotation(..., which = "column")  }

 }

@@ -19,6 +19,7 @@ Draw the single annotation

 }

 \details{

 A viewport is created.

+

 The graphics would be different depending the annotation is a row annotation or a column annotation.

 }

 \value{

@@ -18,8 +18,10 @@ Draw column annotations

 }

 \details{

 A viewport is created which contains column annotations.

+

 Since the column annotations is a \code{\link{HeatmapAnnotation-class}} object, the function

 calls \code{\link{draw,HeatmapAnnotation-method}} to draw the annotations.

+

 This function is only for internal use.

 }

 \value{

@@ -19,6 +19,7 @@ Draw legends for all column annotations

 }

 \details{

 A viewport is created which contains annotation legends.

+

 This function is only for internal use.

 }

 \value{

@@ -22,6 +22,7 @@ Draw row names or column names

 }

 \details{

 A viewport is created which contains row names or column names.

+

 This function is only for internal use.

 }

 \value{

@@ -23,7 +23,9 @@ Draw dendrogram on row or column

 \details{

 If the matrix is split into several row slices, a list of dendrograms will be drawn by 

 the heatmap that each dendrogram corresponds to its row slices.

+

 A viewport is created which contains dendrograms.

+

 This function is only for internal use.

 }

 \value{

@@ -21,7 +21,9 @@ Draw the heatmap body

 The matrix can be split into several parts by rows if \code{km} or \code{split} is 

 specified when initializing the \code{\link{Heatmap}} object. If the matrix is split, 

 there will be gaps between rows to identify different row-slice.

+

 A viewport is created which contains subset rows of the heatmap.

+

 This function is only for internal use.

 }

 \value{

@@ -19,6 +19,7 @@ Draw legends for all heatmaps

 }

 \details{

 A viewport is created which contains heatmap legends.

+

 This function is only for internal use.

 }

 \value{

@@ -17,6 +17,7 @@ Draw the list of heatmaps

 }

 \details{

 A viewport is created which contains heatmaps.

+

 This function is only for internal use.

 }

 \value{

@@ -20,6 +20,7 @@ Draw heatmap title

 }

 \details{

 A viewport is created which contains heatmap title.

+

 This function is only for internal use.

 }

 \value{

@@ -18,6 +18,7 @@ Draw heatmap list title

 }

 \details{

 A viewport is created which contains heatmap list title.

+

 This function is only for internal use.

 }

 \value{

@@ -17,6 +17,7 @@ Get a list of color mapping objects

 }

 \details{

 Color mapping for visible simple annotations are only returned.

+

 This function is only for internal use.

 }

 \value{

@@ -17,6 +17,7 @@ Get a list of color mapping parameters

 }

 \details{

 Color mapping parameters for visible simple annotations are only returned.

+

 This function is only for internal use.

 }

 \value{

@@ -21,6 +21,7 @@ grid.dendrogram(dend, facing = c("bottom", "top", "left", "right"),

 }

 \details{

 The dendrogram tree can be renderred (e.g. by \code{dendextend} package).

+

 A viewport is created which contains the dendrogram.

 }

 \value{

@@ -19,6 +19,7 @@ ht_global_opt(..., RESET = FALSE, READ.ONLY = NULL)

 \details{

 You can set some parameters for all heatmaps/annotations by this global function.

 There are following parameters:

+

 \describe{

   \item{heatmap_row_names_gp}{set \code{row_names_gp} in \code{\link{Heatmap}}.}

   \item{heatmap_column_names_gp}{set \code{column_names_gp} in \code{\link{Heatmap}}.}

@@ -17,6 +17,7 @@ Make cluster on columns

 }

 \details{

 The function will fill or adjust \code{column_hclust} and \code{column_order} slots.

+

 This function is only for internal use.

 }

 \value{

@@ -17,8 +17,10 @@ Make the layout of a single heatmap

 \details{

 The layout of the single heatmap will be established by setting the size of each heatmap components.

 Also functions that make graphics for heatmap components will be recorded.

+

 Whether apply row clustering or column clustering affects the layout, so clustering should be applied 

 first before making the layout.

+

 This function is only for internal use.

 }

 \value{

@@ -43,7 +43,9 @@ Make layout for the complete plot

 }

 \details{

 It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.

+

 The layout for the heatmap list and layout for each heatmap are calculated when drawing the heatmap list.

+

 This function is only for internal use.

 }

 \value{

@@ -17,7 +17,9 @@ Make cluster on rows

 }

 \details{

 The function will fill or adjust \code{row_hclust_list}, \code{row_order_list}, \code{row_title} and \code{matrix_param} slots.

+

 If \code{order} is defined, no clustering will be applied.

+

 This function is only for internal use.

 }

 \value{

@@ -32,6 +32,7 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,

 \details{

 The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to

 visualize information that are stored in a data frame.

+

 There are only a few advanced settings in this function, so the heamtap generated by this functioin

 may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually

 constructing a \code{\link{HeatmapList}} object.

@@ -18,6 +18,7 @@ Prepare the heatmap

 }

 \details{

 The preparation of the heatmap includes following steps:

+

 \itemize{

   \item making clustering on rows if specified (by calling \code{\link{make_row_cluster,Heatmap-method}})

   \item making clustering on columns if specified (by calling \code{\link{make_column_cluster,Heatmap-method}})

@@ -16,6 +16,7 @@ rowAnnotation(...)

 }

 \details{

 The function is identical to

+

   \preformatted{

 HeatmapAnnotation(..., which = "row")  }

 }