heatmap_column_group_labels: Add Heatmap column group labels

In jmw86069/jamses: Jam SummarizedExperiment Stats

Add Heatmap column group labels

Description

Add Heatmap column group labels, specifically for ComplexHeatmap output.

Usage

heatmap_column_group_labels(
  hm_group_list,
  hm_drawn = NULL,
  se = NULL,
  add_group_label = TRUE,
  add_group_line = TRUE,
  add_group_box = FALSE,
  group_line_buffer = grid::unit(1, "mm"),
  group_line_lwd = 2,
  group_line_requires_label = TRUE,
  group_box_lwd = 2,
  group_box_outer = TRUE,
  font_cex = 1,
  hm_title_base = NULL,
  hm_body_base = NULL,
  hm_title_base_default = "centered\nexpression_column_title_",
  hm_body_base_default = "centered\nexpression_heatmap_body_1_",
  y_offset_lines = 0,
  endlines = 1,
  use_gridtext = TRUE,
  verbose = FALSE,
  ...
)

Arguments

hm_group_list	character or list with one of the following types of content: character colnames in the column data of se argument, specifically colnames(colData(se)) to define groupings. list of integer vectors, where list names become labels for each group.
hm_drawn	ComplexHeatmap::HeatmapList object which is returned by the function ComplexHeatmap::draw(). This object is a pointer to the grid graphical elements required.
se	SummarizedExperiment object, required only when hm_group_list is supplied in the form of colnames of the SummarizedExperiment::colData(se).
add_group_label	logical indicating whether to draw the group character label above each group defined in hm_group_list.
add_group_line	logical indicating whether to draw the group line for each group defined in hm_group_list. The line is intended to appear below the text label when add_group_label=TRUE.
add_group_box	logical indicating whether to draw a box around the heatmap region defined by each group in hm_group_list.
group_line_buffer	grid::unit object indicating the whitespace buffer region betwen adjacent lines when add_group_line=TRUE. The default enforces 1-mm white space between lines so they do not touch.
group_line_lwd	numeric line width when add_group_line=TRUE.
group_line_requires_label	logical whether to require the associated group label to contain non-whitespace visible text. group_line_requires_label=TRUE (default) requires group label to have visible characters, which means the presence of an empty labels will cause the group line not to be drawn. group_line_requires_label=FALSE does not require a group label, therefore all group lines are drawn.
group_box_lwd	numeric line width when add_group_box=TRUE.
group_box_outer	logical indicating whether to draw the group box as an outer border, which means the border will be drawn only on the very outer edge of the heatmap body, and will not overlap the heatmap contents. This option is only active when add_group_box=TRUE.
font_cex	numeric adjustment for font sizes overall.
hm_title_base	character string used to search for matching heatmap column title grid layout regions. It is derived from the Heatmap argument name, usually followed by ⁠"_column_title_". When ⁠NULL⁠the default values are defined by⁠detect_heatmap_components()elementcolumn_title_components'.
hm_body_base	character string used to search for matching heatmap body grid layout regions. It is derived from the Heatmap argument name, usually followed by ⁠"_body_1_". When ⁠NULL⁠the default values are defined by⁠detect_heatmap_components()elementheatmap_body_components'. Note: Currently the group box only includes the first row_split, although it is intended to include the entire set of heatmap rows in future iterations.
hm_title_base_default, hm_body_base_default	character string used as reference for hm_title_base,hm_body_base.
y_offset_lines	numeric adjustment used to shift the text label and underline by this many lines of character height. It is mainly used internally for iterative calls, when hm_group_list includes multiple layers of groups. The text and underline are intended to fill 2 character height lines, although this argument can be used to make manual adjustments.
endlines	integer number of blank lines to append to the end of each group label, which has the effect of shifting the group label upwards slightly.
use_gridtext	logical (default TRUE) whether to render text using gridtext::richtext_grob() in order to enable markdown and limited HTML-based formatting.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function is currently experimental, and is intended only for a specific scenario, to augment a ComplexHeatmap::Heatmap object, as produced by heatmap_se(), that used the argument column_split to sub-divide the heatmap columns into subgroups. This function draws labels above the heatmap to describe group factor values associated with column splits.

When there are multiple layers of grouping, this function will also draw multiple layers. For example, when columns are split by column_split=c("Treatment", "Time"), it will produce a heatmap where each column slice has one combination of Treatment and Time. This function can be used to add a layer of labels by "Time", and a layer of labels by "Treatment". The labels are shown by default with a broad underline to indicate contiguous column slices that contain the same "Treatment" or "Time" values.

The output can provide a cleaner visualization than the alternative of displaying colorized annotation boxes at the top of the heatmap.

Input Formats

There are two strategies for defining the column group data to display:

Input using colnames from colData(se)

This option is recommended as the "easiest" method. It requires:

• hm_group_list provides a character vector of colnames(colData(se)). Note that the columns are applied bottom-to-top, so it is sometimes helpful to supply columns in reverse order for column_split.

• se must be provided, since it supplies colData(se)

Each value in hm_group_list is applied from bottom-to-top, to define a row of labels. By default, add_group_line=TRUE, so labels are also underlined to indicate samples included in each group.

Input using a named list

This option is recommended when labeling a subset of column slices, or when the column slice groups need to be customized in some way.

Additional requirements

• The Heatmap column_title should (usually) be empty, so that no text labels are drawn which may overlap the labels drawn by this function. Use column_title=" " (with a whitespace character) to prevent ComplexHeatmap::Heatmap() from using its internal default text label.

• There usually needs to be whitespace above the heatmap, which can be accomplished when drawing a Heatmap object hm like this: ComplexHeatmap::draw(hm, column_title="\n\n\n\n")

• When also displaying a heatmap title as defined by heatmap_se(), the adjustment can be done like this:

ComplexHeatmap::draw(hm,
   column_title=paste0(attr(hm, "hm_title"),
      "\n\n\n\n"))

• The arguments hm_title_base and hm_body_base should match the heatmap name, which is defined in heatmap_se() with data_type, usually prefixed "centered\n" when the data is centered by that function. For example, when data_type="abundance", the corresponding argument value should be hm_title_base="centered\nabundance_column_title_".

• use detect_heatmap_components() to help identify the appropriate grid elements available to be used by this function.

When the heatmap contains "column_title" elements defined in ComplexHeatmap::list_components(), and there is no element "global_column_title", the y_offset_lines is adjusted down so that the position is inside the column_title region, typically below the column_title when using trailing whitespace (see argument hm_title_buffer in heatmap_se()). However, when element "global_column_title" is present, the y_offset_lines are not adjusted, so that the position is above the column_title region. In this case, to position the labels below the column_title, you can adjust y_offset_lines down manually like this: y_offset_lines=-9.

Todo

• Automate determining the column_title grid layout name.

  • Specifically when only one heatmapname_column_title_1 is present, but there are multiple column groups, it should take the x-axis coordinate values (left and right boundaries) from the heatmap body instead of the column_title region.

• When add_group_box=TRUE, and row_split indicates multiple row groups, it should calculate the y-axis coordinate values (top and bottom boundaries) using the full set of row groups.

• Enable blank annotations, either by passing a subset se, or by annotations with no associated label.

jmw86069/jamses documentation built on May 31, 2024, 1:36 p.m.