pheatmap {ComplexHeatmap} | R Documentation

## Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap

### Description

Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap

### Usage

    pheatmap(mat,
        color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
        kmeans_k = NA,
        breaks = NA,
        border_color = ifelse(nrow(mat) < 100 & ncol(mat) < 100, "grey60", NA),
        cellwidth = NA,
        cellheight = NA,
        scale = "none",
        cluster_rows = TRUE,
        cluster_cols = TRUE,
        clustering_distance_rows = "euclidean",
        clustering_distance_cols = "euclidean",
        clustering_method = "complete",
        clustering_callback = NA,
        cutree_rows = NA,
        cutree_cols = NA,
        treeheight_row = ifelse(class(cluster_rows) == "hclust" || cluster_rows, 50, 0),
        treeheight_col = ifelse(class(cluster_cols) == "hclust" || cluster_cols, 50, 0),
        legend = TRUE,
        legend_breaks = NA,
        legend_labels = NA,
        annotation_row = NA,
        annotation_col = NA,
        annotation = NA,
        annotation_colors = NA,
        annotation_legend = TRUE,
        annotation_names_row = TRUE,
        annotation_names_col = TRUE,
        drop_levels = TRUE,
        show_rownames = TRUE,
        show_colnames = TRUE,
        main = NA,
        fontsize = 10,
        fontsize_row = fontsize,
        fontsize_col = fontsize,
        angle_col = c("270", "0", "45", "90", "315"),
        display_numbers = FALSE,
        number_format = "%.2f",
        number_color = "grey30",
        fontsize_number = 0.8 * fontsize,
        gaps_row = NULL,
        gaps_col = NULL,
        labels_row = NULL,
        labels_col = NULL,
        filename = NA,
        width = NA,
        height = NA,
        silent = FALSE,
        na_col = "#DDDDDD",
        name = NULL,

        # argument specific for Heatmap()
        heatmap_legend_param = list(),
        ...,
        run_draw = FALSE)

### Arguments

`mat` | The input matrix.
`color` | The same as in `pheatmap`. Here you don't necessarily need to generate a long color vector. The discrete colors sent to `colorRampPalette` are also OK here. E.g. `colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100)` can be simply replaced as `rev(brewer.pal(n = 7, name = "RdYlBu"))`.
`kmeans_k` | The same as in `pheatmap`.
`breaks` | The same as in `pheatmap`.
`border_color` | The same as in `pheatmap`.
`cellwidth` | The same as in `pheatmap`.
`cellheight` | The same as in `pheatmap`.
`scale` | The same as in `pheatmap`.
`cluster_rows` | The same as in `pheatmap`.
`cluster_cols` | The same as in `pheatmap`.
`clustering_distance_rows` | The same as in `pheatmap`.
`clustering_distance_cols` | The same as in `pheatmap`.
`clustering_method` | The same as in `pheatmap`.
`clustering_callback` | The same as in `pheatmap`.
`cutree_rows` | The same as in `pheatmap`.
`cutree_cols` | The same as in `pheatmap`.
`treeheight_row` | The same as in `pheatmap`.
`treeheight_col` | The same as in `pheatmap`.
`legend` | The same as in `pheatmap`.
`legend_breaks` | The same as in `pheatmap`.
`legend_labels` | The same as in `pheatmap`.
`annotation_row` | The same as in `pheatmap`.
`annotation_col` | The same as in `pheatmap`.
`annotation` | The same as in `pheatmap`.
`annotation_colors` | The same as in `pheatmap`.
`annotation_legend` | The same as in `pheatmap`.
`annotation_names_row` | The same as in `pheatmap`.
`annotation_names_col` | The same as in `pheatmap`.
`drop_levels` | Enforced to be `TRUE`.
`show_rownames` | The same as in `pheatmap`.
`show_colnames` | The same as in `pheatmap`.
`main` | The same as in `pheatmap`.
`fontsize` | The same as in `pheatmap`.
`fontsize_row` | The same as in `pheatmap`.
`fontsize_col` | The same as in `pheatmap`.
`angle_col` | The same as in `pheatmap`.
`display_numbers` | The same as in `pheatmap`.
`number_format` | The same as in `pheatmap`.
`number_color` | The same as in `pheatmap`.
`fontsize_number` | The same as in `pheatmap`.
`gaps_row` | The same as in `pheatmap`.
`gaps_col` | The same as in `pheatmap`.
`labels_row` | The same as in `pheatmap`.
`labels_col` | The same as in `pheatmap`.
`filename` | Not supported.
`width` | Not supported.
`height` | Not supported.
`silent` | Not supported.
`na_col` | The same as in `pheatmap`.
`name` | Name of the heatmap. This argument is passed to `Heatmap`.
`heatmap_legend_param` | Pass to `Heatmap`.
`...` | Other arguments passed to `Heatmap`.
`run_draw` | Whether to run `draw()` function to the heatmap object.

### Details

This function aims to execute `pheatmap::pheatmap` code purely with ComplexHeatmap.

### Value

A `Heatmap-class` object.

### See Also

See https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/

`compare_pheatmap` that compares heatmaps between `pheatmap::pheatmap()` and `ComplexHeatmap::pheatmap()`.

### Examples

    # There is no example
    NULL

[Package ComplexHeatmap version 2.10.0 Index]