oncoPrint: Make oncoPrint
In eilslabs/ComplexHeatmap: Making Complex Heatmaps

Description Usage Arguments Details Value Author(s) Examples

Make oncoPrint

oncoPrint(mat, get_type = function(x) x,
    alter_fun = alter_fun_list, alter_fun_list = NULL, col,
    row_order = oncoprint_row_order(),
    column_order = oncoprint_column_order(),
    show_pct = TRUE, pct_gp = row_names_gp, pct_digits = 0,
    axis_gp = gpar(fontsize = 8),
    show_row_barplot = TRUE,
    row_barplot_width = unit(2, "cm"),
    remove_empty_columns = FALSE,
    heatmap_legend_param = list(title = "Alterations"),
    top_annotation = HeatmapAnnotation(column_bar = anno_oncoprint_barplot(),
    annotation_height = unit(2, "cm")),
    top_annotation_height = top_annotation@size,
    bottom_annotation = new("HeatmapAnnotation"),
    bottom_annotation_height = bottom_annotation@size,
    barplot_ignore = NULL,
    row_title = character(0),
    row_title_side = c("left", "right"),
    row_title_gp = gpar(fontsize = 14),
    row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),
    column_title = character(0),
    column_title_side = c("top", "bottom"),
    column_title_gp = gpar(fontsize = 14),
    column_title_rot = 0,
    show_row_names = TRUE,
    row_names_gp = gpar(fontsize = 12),
    show_column_names = FALSE,
    column_names_gp = gpar(fontsize = 12),
    split = NULL,
    gap = unit(1, "mm"),
    combined_name_fun = function(x) paste(x, collapse = "/"),
    width = NULL,
    ...)

`mat`	a character matrix which encodes mulitple alterations or a list of matrix for which every matrix contains binary value representing the alteration is present or absent. When it is a list, the names 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, this self-defined function determines how to extract them. Only work when `mat` is a matrix.
`alter_fun`	a single function or a list of functions which define how to add graphics for different alterations. If it is a list, the names of the list should cover all alteration types.
`alter_fun_list`	deprecated, use `alter_run` instead.
`col`	a vector of color for which names correspond to alteration types.
`row_order`	order of genes. By default it is sorted by frequency of alterations decreasingly. Set it to `NULL` if you don't want to set the order
`column_order`	order of samples. By default the order is calculated by the 'memo sort' method which can visualize the mutual exclusivity across genes. Set it to `NULL` if you don't want to set the order
`show_pct`	whether show percent values on the left of the oncoprint
`pct_gp`	graphic paramters for percent row annotation
`pct_digits`	digits for percent values
`axis_gp`	graphic paramters for axes
`show_row_barplot`	whether show barplot annotation on rows
`row_barplot_width`	width of barplot annotation on rows. It should be a `unit` object
`remove_empty_columns`	if there is no alteration in that sample, whether remove it on the heatmap
`heatmap_legend_param`	pass to `Heatmap`
`top_annotation`	by default the top annotation contains barplots representing frequency of mutations in every sample.
`top_annotation_height`	total height of the column annotations on the top.
`bottom_annotation`	a `HeatmapAnnotation` object.
`bottom_annotation_height`	total height of the column annotations on the bottom.
`barplot_ignore`	specific alterations that you don't want to put on the barplots. If you want to really suppress the top barplot set `top_annotation` to `NULL`.
`row_title`	title on row.
`row_title_side`	will the title be put on the left or right of the heatmap?
`row_title_gp`	graphic parameters for drawing text.
`row_title_rot`	rotation of row titles. Only 0, 90, 270 are allowed to set.
`column_title`	title on column.
`column_title_side`	will the title be put on the top or bottom of the heatmap?
`column_title_gp`	graphic parameters for drawing text.
`column_title_rot`	rotation of column titles. Only 0, 90, 270 are allowed to set.
`show_row_names`	whether show row names.
`row_names_gp`	graphic parameters for drawing text.
`show_column_names`	whether show column names.
`column_names_gp`	graphic parameters for drawing text.
`split`	a vector or a data frame by which the rows are split. But if `cluster_rows` is a clustering object, `split` can be a single number indicating rows are to be split according to the split on the tree.
`gap`	gap between row-slices if the heatmap is split by rows, should be `unit` object. If it is a vector, the order corresponds to top to bottom in the heatmap
`combined_name_fun`	if the heatmap is split by rows, how to make a combined row title for each slice? The input parameter for this function is a vector which contains level names under each column in `split`.
`width`	the width of the single heatmap, should be a fixed `unit` object. It is used for the layout when the heatmap is appended to a list of heatmaps.
`...`	pass to `Heatmap`, so can set `bottom_annotation` here.