barcode_ggheatmap {barcodetrackR} | R Documentation

## barcode_ggheatmap

### Description

Creates a heatmap displaying the log abundance of the top 'n' clones from each sample in the Summarized Experiment object, using ggplot2. Clones are on the y-axis and samples are on the x-axis. The ordering and clustering of clones on the y-axis as well as all aesthetics of the plot can be controlled through the arguments described below.

### Usage

    barcode_ggheatmap(
      your_SE,
      plot_labels = NULL,
      n_clones = 10,
      cellnote_assay = "stars",
      your_title = NULL,
      grid = TRUE,
      label_size = 12,
      dendro = FALSE,
      cellnote_size = 4,
      distance_method = "Euclidean",
      minkowski_power = 2,
      hclust_linkage = "complete",
      row_order = "hierarchical",
      clusters = 0,
      percent_scale = c(0, 2.5e-05, 0.001, 0.01, 0.1, 1),
      color_scale = c("#4575B4", "#4575B4", "lightblue", "#fefeb9", "#D73027", "red4"),
      return_table = FALSE
    )

### Arguments

`your_SE` | A Summarized Experiment object.
`plot_labels` | Vector of x axis labels. Defaults to colnames(your_SE).
`n_clones` | The top 'n' clones to plot.
`cellnote_assay` | Character. One of "stars", "counts", or "proportions." To have no cellnote, set cellnote_size to 0.
`your_title` | The title for the plot.
`grid` | Logical. Include a grid or not in the heatmap.
`label_size` | The size of the column labels.
`dendro` | Logical. Whether or not to show row dendrogram when hierarchical clustering.
`cellnote_size` | The numerical size of the cell note labels. To have no cellnote, set cellnote_size to 0.
`distance_method` | Character. Use summary(proxy::pr_DB) to see all possible options for distance metrics in clustering.
`minkowski_power` | The power of the Minkowski distance (if minkowski is the distance method used).
`hclust_linkage` | Character. One of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
`row_order` | Character; "hierarchical" to perform hierarchical clustering on the output and order in that manner, "emergence" to organize rows by order of presence in data (from left to right), or a character vector of rows within the summarized experiment to plot.
`clusters` | How many clusters to cut hierarchical tree into for display when row_order is "hierarchical".
`percent_scale` | A numeric vector through which to spread the color scale (values inclusive from 0 to 1). Must be same length as color_scale.
`color_scale` | A character vector which indicates the colors of the color scale. Must be same length as percent_scale.
`return_table` | Logical. Whether or not to return table of barcode sequences with their log abundance in the 'value' column and cellnote for each sample instead of displaying a plot.

### Value

Displays a heatmap in the current plot window. Or if return_table is set to TRUE, returns a dataframe of the barcode sequences, log abundances, and cellnotes for each sample.

### Examples

    data(wu_subset)
    barcode_ggheatmap(
        your_SE = wu_subset, n_clones = 10,
        grid = TRUE, label_size = 6
    )

[Package barcodetrackR version 1.2.0 Index]