plot_optimal_CORE {scGPS} | R Documentation

## plot one single tree with the optimal clustering result

### Description

after an optimal cluster has been identified, users may use this function to plot the resulting dendrogram with the branch colors represent clutering results

### Usage

    plot_optimal_CORE(
      original_tree,
      optimal_cluster = NULL,
      shift = -100,
      values = NULL
    )

### Arguments

`original_tree` | a dendrogram object
`optimal_cluster` | a vector of cluster IDs for cells in the dendrogram
`shift` | a numer specifying the gap between the dendrogram and the colored
`values` | a vector containing color values of the branches and the colored bar underneath the tree bar underneath the dendrogram. This parameter allows better selection of colors for the display.

### Value

a plot with colored braches and bars for the optimal clustering result

### Author(s)

Quan Nguyen, 2017-11-25

### Examples

    day5 <- day_5_cardio_cell_sample
    mixedpop2 <-new_summarized_scGPS_object(ExpressionMatrix = day5$dat5_counts,
        GeneMetadata = day5$dat5geneInfo, CellMetadata = day5$dat5_clusters)
    CORE_cluster <- CORE_clustering(mixedpop2, remove_outlier = c(0))
    key_height <- CORE_cluster$optimalClust$KeyStats$Height
    optimal_res <- CORE_cluster$optimalClust$OptimalRes
    optimal_index = which(key_height == optimal_res)
    plot_optimal_CORE(original_tree= CORE_cluster$tree,
        optimal_cluster = unlist(CORE_cluster$Cluster[optimal_index]),
        shift = -2000)

[Package scGPS version 1.8.0 Index]