ComplexHeatmap: oncoPrint – R documentation

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ComplexHeatmap

oncoPrint

Make oncoPrint

Description

Make oncoPrint

Usage

oncoPrint(mat,
    get_type = default_get_type,
    alter_fun,
    alter_fun_is_vectorized = NULL,
    col = NULL,
    
    top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot()),
    right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot()),
    left_annotation = NULL,
    bottom_annotation = NULL,
    
    show_pct = TRUE,
    pct_gp = gpar(fontsize = 10),
    pct_digits = 0,
    pct_side = "left",
    
    row_labels = NULL,
    show_row_names = TRUE,
    row_names_side = "right",
    row_names_gp = pct_gp,
    row_split = NULL,
    
    column_labels = NULL,
    column_names_gp = gpar(fontsize = 10),
    column_split = NULL,
    
    row_order = NULL,
    column_order = NULL,
    cluster_rows = FALSE,
    cluster_columns = FALSE,
    
    remove_empty_columns = FALSE,
    remove_empty_rows = FALSE,
    show_column_names = FALSE,
    heatmap_legend_param = NULL,
    ...)

Arguments

`mat`	The value should be a character matrix which encodes mulitple alterations or a list of matrices for which every matrix contains binary value representing whether the alteration is present or absent. When the value is a list, the names of the list represent alteration types. You can use `unify_mat_list` to make all matrix having same row names and column names.
`get_type`	If different alterations are encoded in the matrix as complex strings, this self-defined function determines how to extract them. It only works when `mat` is a matrix. The default value is `default_get_type`.
`alter_fun`	A single function or a list of functions which defines how to add graphics for different alterations. You can use `alter_graphic` to automatically generate for rectangles and points.
`alter_fun_is_vectorized`	Whether `alter_fun` is implemented vectorized. Internally the function will guess.
`col`	A vector of color for which names correspond to alteration types.
`top_annotation`	Annotation put on top of the oncoPrint. By default it is barplot which shows the number of genes with a certain alteration in each sample.
`right_annotation`	Annotation put on the right of the oncoPrint. By default it is barplot which shows the number of samples with a certain alteration in each gene.
`left_annotation`	Annotation put on the left of the oncoPrint.
`bottom_annotation`	Annotation put at the bottom of the oncoPrint.
`show_pct`	whether show percent values on the left of the oncoprint?
`pct_gp`	Graphic paramters for percent values
`pct_digits`	Digits for the percent values.
`pct_side`	Side of the percent values to the oncoPrint. This argument is currently disabled.
`row_labels`	Labels as the row names of the oncoPrint.
`show_row_names`	Whether show row names?
`row_names_side`	Side of the row names to the oncoPrint. This argument is currently disabled.
`row_names_gp`	Graphic parameters for the row names.
`row_split`	Pass to `Heatmap`.
`column_labels`	Pass to `Heatmap`.
`column_names_gp`	Pass to `Heatmap`.
`column_split`	Pass to `Heatmap`.
`row_order`	Order of rows. By default rows are sorted by the number of occurence of the alterations.
`cluster_rows`	If it is set, it must be a dendrogram/hclust object.
`cluster_columns`	If it is set, it must be a dendrogram/hclust object.
`column_order`	Order of columns. By default the columns are sorted to show the mutual exclusivity of alterations.
`remove_empty_columns`	If there is no alteration in some samples, whether remove them on the oncoPrint?
`remove_empty_rows`	If there is no alteration in some samples, whether remove them on the oncoPrint?
`show_column_names`	Whether show column names?
`heatmap_legend_param`	pass to `Heatmap`.
`...`	Pass to `Heatmap`.

Details

The 'memo sort' method is from https://gist.github.com/armish/564a65ab874a770e2c26 . Thanks to B. Arman Aksoy for contributing the code.

https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html gives details for configuring a oncoPrint.

Value

A Heatmap-class object which means you can add other heatmaps or annotations to it.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL

ComplexHeatmap

Make Complex Heatmaps

v2.6.2

MIT + file LICENSE

Authors

Zuguang Gu

Initial release

2020-11-12

oncoPrint

Description

Usage

Arguments

Details

Value

Author(s)

Examples

ComplexHeatmap

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