plot_CORE: Plot dendrogram tree for CORE result

In scGPS: A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Description

This function plots CORE and all clustering results underneath

Usage

plot_CORE(original.tree, list_clusters = NULL, color_branch = NULL)

Arguments

original.tree	the original dendrogram before clustering
list_clusters	a list containing clustering results for each of the
color_branch	is a vector containing user-specified colors (the number of unique colors should be equal or larger than the number of clusters). This parameter allows better selection of colors for the display.

Value

a plot with clustering bars underneath the tree

Examples

day5 <- day_5_cardio_cell_sample
cellnames <- colnames(day5$dat5_counts)
cluster <-day5$dat5_clusters
cellnames <-data.frame('Cluster'=cluster, 'cellBarcodes' = cellnames)
mixedpop2 <-new_summarized_scGPS_object(ExpressionMatrix = day5$dat5_counts,
    GeneMetadata = day5$dat5geneInfo, CellMetadata = cellnames)
CORE_cluster <- CORE_clustering(mixedpop2, remove_outlier = c(0))
plot_CORE(CORE_cluster$tree, CORE_cluster$Cluster)

scGPS documentation built on Nov. 8, 2020, 5:22 p.m.