plot_clusters: Plots kinetic clusters of genes.

Description Usage Arguments Value Examples

Description

returns a ggplot2 object showing the shapes of the expression patterns followed by a set of pre-selected genes. The topographic lines highlight the distributions of the kinetic patterns relative to overall trend lines.

Usage

1
2
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

1
2
3
4
5
6
7
8
## Not run: 
full_model_fits <- fitModel(HSMM_filtered[sample(nrow(fData(HSMM_filtered)), 100),],  
   modelFormulaStr="~VGAM::bs(Pseudotime)")
expression_curve_matrix <- responseMatrix(full_model_fits)
clusters <- clusterGenes(expression_curve_matrix, k=4)
plot_clusters(HSMM_filtered[ordering_genes,], clusters)

## End(Not run)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.