oncoPrint {ComplexHeatmap} | R Documentation

## Make oncoPrint

### Description

Make oncoPrint

### Usage

    oncoPrint(mat, name,
        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.
`name` | Name of the oncoPrint. Not necessary to specify.
`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

[Package ComplexHeatmap version 2.10.0 Index]