monocle (version 1.6.2)

plot_clusters: Plots the minimum spanning tree on cells.

Description

Plots the minimum spanning tree on cells.

Usage

plot_clusters(cds, clustering, drawSummary = TRUE, sumFun = mean_cl_boot,
  ncol = NULL, nrow = NULL, row_samples = NULL, callout_ids = NULL)

Arguments

cds

CellDataSet for the experiment

clustering

a clustering object produced by clusterCells

drawSummary

whether to draw the summary line for each cluster

sumFun

whether the function used to generate the summary for each cluster

ncol

number of columns used to layout the faceted cluster panels

nrow

number of columns used to layout the faceted cluster panels

row_samples

how many genes to randomly select from the data

callout_ids

a vector of gene names or gene ids to manually render as part of the plot

Value

• a ggplot2 plot object

Examples

full_model_fits <- fitModel(HSMM_filtered[sample(nrow(fData(HSMM_filtered)), 100),],  modelFormulaStr="expression~VGAM::bs(Pseudotime)")
expression_curve_matrix <- responseMatrix(full_model_fits)
clusters <- clusterGenes(expression_curve_matrix, k=4)
plot_clusters(HSMM_filtered[ordering_genes,], clusters)