mds_plot {barcodetrackR} | R Documentation

## MDS Plot

### Description

Calculates a simmilarity/dissimlarity index or metrix for each sample-sample pair and reduces the resulting dist matrix into two dimensions

### Usage

    mds_plot(
      your_SE,
      group_by = "SAMPLENAME",
      method_dist = "bray",
      assay = "proportions",
      your_title = NULL,
      point_size = 3,
      text_size = 12,
      return_table = FALSE,
      kmeans_cluster = FALSE,
      k.param = 3,
      draw_ellipses = FALSE
    )

### Arguments

`your_SE` | Summarized Experiment object containing clonal tracking data as created by the barcodetrackR 'create_SE' function.
`group_by` | Column of metadata to color samples by. Can also specify "kmeans_cluster" if kmeans_cluster argument is set to TRUE, and then the grouping variables will be the clusterinng result.
`method_dist` | Dissimilarity index from vegan. One of "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", or "cao".
`assay` | The assay to calculate the index on
`your_title` | Character. The title for the plot.
`point_size` | Numeric. The size of the points.
`text_size` | Numeric. Size of text in plot.
`return_table` | Logical. If set to true, the function will return a dataframe containing each samples reduced measure of dissimilarity coordinates.
`kmeans_cluster` | Logical. If set to true, each sample will be assigned a cluster computed by kmeans on the chosen assay.
`k.param` | Numeric. If kmeans_cluster is TRUE, provide the number of kmeans clusters to identify.
`draw_ellipses` | Logical. If kmeans_cluster is TRUE, draw ellipses around the different kmeans clusters.

### Value

Plots dissimilarity indices between samples in your_SE. Or if return table is set to TRUE, returns a dataframe of each sample's reduced measures of dissimilarity coordinates.

### Examples

    data(wu_subset)
    mds_plot(your_SE = wu_subset, method_dist = "bray", group_by = "celltype")
    # "

[Package barcodetrackR version 1.0.0 Index]