heatmap_plot {hipathia} | R Documentation

## Plots subpathways heatmap

### Description

Plots a heatmap with the values of the subpathways.

### Usage

    heatmap_plot(data, group = NULL, sel_assay = 1, colors = "classic",
      sample_clust = TRUE, variable_clust = FALSE, labRow = NULL,
      labCol = NULL, sample_colors = NULL, scale = TRUE, save_png = NULL,
      legend = TRUE, legend_xy = "topright", pch = 15, main = NULL)

### Arguments

`data` | Either a SummarizedExperiment or a matrix with the values to be plotted. Rows are features and columns are samples.
`group` | Either a character indicating the name of the column in colData including the classes to plot, or a character vector with the class to which each sample belongs. Samples must be ordered as in `data`. By default, all samples will be assigned to the same class.
`sel_assay` | Character or integer, indicating the assay to be normalized in the SummarizedExperiment. Default is 1.
`colors` | Either a character vector with colors or a key name indicating the color scheme to be used in the heatmap. If a character vector is provided, it is recommended to provide at least 3 colors. Three different predefined color schemes may be selected by providing a key name. Options are: * `classic` Blue for lower values, white for medium values, red for higher values. * `hipathia` Hipathia predefined color scheme: Green for lower values, white for medium values, orange for higher values. * `redgreen` Green for lower values, black for medium values, red for higher values. By default `classic` color scheme is applied.
`sample_clust` | Boolean, whether to cluster samples (columns). By default TRUE.
`variable_clust` | Boolean, whether to cluster variables (rows). By default FALSE. If TRUE, rows with 0 variance are removed.
`labRow, labCol` | Character vectors with row and column labels to be used. By default rownames(data) or colnames(data) are used, respectively.
`sample_colors` | Named character vector of colors. The names of the colors must be the classes in `group`. Each sample will be assigned the color corresponding to its class, taken from the `group` vector. By default a color will be assigned automatically to each class.
`scale` | Boolean, whether to scale each row to the interval [0,1]. Default is TRUE.
`save_png` | Path to the file where the image as PNG will be saved. By default, the image is not saved.
`legend` | Boolean, whether to display a legend.
`legend_xy` | Position for the legend, in case `legend` is TRUE.
`pch` | Graphical parameter from `par()` function.
`main` | Main title of the image

### Value

Heatmap of the values of the subpathways

### Examples

    data(brca_design)
    data(path_vals)
    sample_group <- brca_design[colnames(path_vals),"group"]
    heatmap_plot(path_vals, group = sample_group)
    heatmap_plot(path_vals, group = sample_group, colors = "hipathia",
    variable_clust = TRUE)

[Package hipathia version 1.4.1 Index]