generateEnrichedHeatmap: generateEnrichedHeatmap

In RockefellerUniversity/profileplyr: Visualization and annotation of read signal over genomic ranges with profileplyr

generateEnrichedHeatmap

Description

export a profileplyr object directly to an object of the EnrichedHeatmap class

Usage

generateEnrichedHeatmap(
  object,
  include_group_annotation = TRUE,
  extra_annotation_columns = NULL,
  sample_names = NULL,
  return_ht_list = FALSE,
  ylim = "common_max",
  top_anno_height = unit(2, "cm"),
  samples_to_sortby = NULL,
  decreasing = FALSE,
  all_color_scales_equal = TRUE,
  matrices_color = NULL,
  color_by_sample_group = NULL,
  matrices_pos_line = FALSE,
  matrices_pos_line_gp = gpar(lty = 2),
  top_anno_axis_font = gpar(fontsize = 8),
  matrices_column_title_gp = gpar(fontsize = 8, fontface = "bold"),
  matrices_axis_name = NULL,
  matrices_axis_name_gp = gpar(fontsize = 8),
  group_anno_color = NULL,
  group_anno_width = 3,
  group_anno_row_title_gp = gpar(fontsize = 10),
  group_anno_column_names_gp = gpar(fontsize = 10),
  extra_anno_color = vector(mode = "list", length = length(extra_annotation_columns)),
  extra_anno_top_annotation = TRUE,
  extra_anno_width = (rep(6, length(extra_annotation_columns))),
  only_extra_annotation_columns = FALSE,
  gap = 2,
  genes_to_label = NULL,
  gene_label_font_size = 6,
  show_heatmap_legend = NULL,
  legend_params = list(),
  use_raster = length(object) > 2000,
  raster_device = "CairoPNG",
  raster_quality = 2,
  raster_device_param = list()
)

Arguments

object	A profileplyr object
include_group_annotation	If TRUE (default value) then the Heatmap will be grouped based on the range metadata column specified by 'rowGroupsInUse'
extra_annotation_columns	A character vector of names that match column names of mcols(object). Extra annotation columns will be added to the heatmap based on the values of these indicated range metadata columns.
sample_names	A character vector that will set the names of the heatmap components that are generated from the profileplyr assays() matrices. This argument is optional, by default the names will be the name of the samples in the profileplyr object rownames(sampleData(object)).
return_ht_list	Whether the returned object is the heatmap list and not the actual figure. This will be a list of the various components (heatmaps and annotation columns) that can be added to with additional columns in a customized manner.
ylim	A numeric vector of two numbers that specifies the minimum and maximum of the yaxis of all the heatmaps generated for the matrices. The default is to use the max of the heatmap with the highest signal (ylim = 'common_max'). If ylim = NULL, different ranges will be inferred for each heatmap. If ylim is a single numeric vector, then that range will be used for all heatmaps. Different ranges can be set for each heatmap by making ylim a list that is the same length as the number of heatmaps/matrices, with each element of the list corresponding to each heatmap. Lastly, ylim can be a character string matching a column name in sampleData(object), and this will make the heatmaps with the same grouping have the same ylims as determined by the common max within groups.
top_anno_height	The height (as a unit object) of the top annotation of all heatmaps representing the matrices
samples_to_sortby	Only relevant if object@params$mcolToOrderBy is NULL (i.e it hasn't been changed), meaning that the rows are sorted by the mean signal of all heatmaps. This argument allows sorting by the mean of a subset of samples, and should be either a character or numeric vector. If numeric, then the samples/matrices that have that index in the profileplyr object will be used to order the rows of the heatmap. If a character vector, then the elements must match the name of a sample in the object (rownames(sampleData(object))), and these samples will be used to order the heatmap.
decreasing	If object@params$mcolToOrderBy has been changed and is not NULL, then the ranges will be ordered by the column indicated in this slot of the metadata. By default, the order will be increasing for the factor or numeric value. For decreasing order, choose decreasing = TRUE.
all_color_scales_equal	If TRUE (default value) then the same color scale will be used for each separate heatmap. If FALSE, color scales will be inferred for each heatmap as indicated by the legends.
matrices_color	Either a single character vector, a numeric vector, a function call to colorRamp2 from the circlize package, or a list. For anything but a list, all the heatmaps generated for the matrices of the profileplyr object will be the same and will be colored as specified here. The character and numeric vector inputs must be either two or three elements in length (denoting color progressions - three elements will give a middle color break), and each element must be a character string or number that points to a color. By default, numeric vectors use the colors in palette(), however this can be expanded with other R color lists(e.g. colors()). If this argument is a list then it's length must equal the number of matrices/samples that exist in the input profileplyr object. The components of the list can be either a numeric vector, character vector, or color function (they do not have to all be the same type of specification). Each element in the list will be the color mapping to the corresponding element in the profileplyr object.
color_by_sample_group	A character vector that is identical to a column name in sampleData(object), and if set, the heatmaps will be colored based on that column (should be a factor, if not it will be converted to one)
matrices_pos_line	A logical for whether to draw a vertical line(s) at the position of the target (for both a single point or a window). Default is true.
matrices_pos_line_gp	Graphics parameters for the vertical position lines. Should be set with the gpar() function from the grid() package.
top_anno_axis_font	The fontsize of the y-axis labels for the top annotation of all heatmaps representing the matrices
matrices_column_title_gp	Graphics parameters for the titles on top of each range/matrix. Should be set with the gpar() function from the grid() package.
matrices_axis_name	Names for axis which is below the heatmap. For profileplyr object made from BamBigwig_to_chipProfile/as_profileplyr functions, the names will be of length three, with the middle point being the midpoint of each range. If the profileplyr object was made from a deeptools matrix with import_deepToolsMat(), the names will be length three if matrix was generated with 'computeMatrix reference-point', or length of four if matrix was generated with 'computeMatrix scale-regions' corresponding to upstream, start of targets, end of targets and downstream (or length of two if no upstream/downstream included).
matrices_axis_name_gp	Graphics parameters for the text on the x-axis of each matrix heatmap. Should be set with the gpar() function from the grid() package.
group_anno_color	This will specify colors for the grouping column if the 'include_group_annotation' argument is set to TRUE. Since the group column of the range metadata should always be a discrete value, this should be either a numeric vector or character vector with color names. By default, numeric vectors use the colors in palette(), however this can be expanded with other R color lists(e.g. colors()). The length of this vector must equal the number of groups.
group_anno_width	A numeric value that is used to will set the width of the column bar (in mm using the unit() function from the grid package) for the grouping annotation column.
group_anno_row_title_gp	Graphics parameters for the labels of the groups on the side of the heatmap. Should be set with the gpar() function from the grid() package.
group_anno_column_names_gp	Graphics parameters for the label of the grouping annotation column. Should be set with the gpar() function from the grid() package.
extra_anno_color	This will specify colors for the annotation columns added by the 'extra_annotation_columns' argument. This must be a list that is of equal length to the 'extra_annotation_columns' argument. Each element of this list will be used to specify the color scheme for the corresponding element of the 'extra_annotation_columns' vector. If an element is NULL, the default colors will be used for the column annotation. For a column with discrete variables this will typically be a vector of numbers or a vector of color names. By default, numeric vectors use the colors in palette(), however this can be expanded with other R color lists(e.g. colors()). For columns with continuous variables, this can also be a a vector of numbers or a vector of color names to signify the color progression, or it can be color mapping function using colorRamp2() from the circlize package.
extra_anno_top_annotation	This is a logical vector that determines whether annotation plots are shown on top of the heatmaps for the extra annotations. This must either be a length of 1, in which case all of the heatmaps will abide by this value. Otherwise this must be a vector of equal length to the 'extra_annotation_columns' argument and the elements of this vector will correspond to the equivalent elements in 'extra annotation_columns'
extra_anno_width	This will set the width of the individual extra annotation columns on the right side of the figure. This must be a numeric vector with each element setting the width for the corresponding element in the 'extra_annotation_columns' argument.
only_extra_annotation_columns	If set to TRUE, only the heatmaps representing the extra annotation columns will be shown, and the range based heatmaps from the assay matrices will be excluded.
gap	The size of the gap between heatmaps and annotations. Only relevant if return_ht_list = FALSE
genes_to_label	A character vector of gene symbols that should match character strings in the 'SYMBOL' column that results from either 'annotateRanges' or 'annotateRanges_great'. Genes that are both in this vector and in the 'SYMBOL' column will be labeled on the heatmap.
gene_label_font_size	The size of the text for the labels for genes specified in 'genes_to_label' argument.
show_heatmap_legend	A logical vector with each position corresponding to each matrix heatmap (not including the 'extra_annotation_columns') that determines whether a legend is produced for that heatmap. By default a single legend is made if all heatmaps use the same color scale, or separate legends are made for each matrix heatmap if the scales are different.
legend_params	A list that contains parameters for the legend. See color_mapping_legend-ColorMapping-method for all available parameters.
use_raster	Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.
raster_device	Graphic device which is used to generate the raster image. Options are "png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"
raster_quality	A value set to larger than 1 will improve the quality of the raster image.
raster_device_param	A list of further parameters for the selected graphic device. For raster image support, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image .

Details

Takes a profileplyr object and generates a heatmap that can be annotated by group or by range metadata columns of the profileplyr object

Value

By default a customized version of a heatmap from EnrichedHeatmap, if return_ht_list = TRUE then a heatmap list is returned that can be modified and then entered as an input for the EnrichedHeatmap function

Examples

example <- system.file("extdata", "example_deepTools_MAT", package = "profileplyr") 
object <- import_deepToolsMat(example)

generateEnrichedHeatmap(object, include_group_annotation = FALSE)

RockefellerUniversity/profileplyr documentation built on Jan. 28, 2023, 10:09 a.m.