plot_clusters {monocle} | R Documentation

## Plots kinetic clusters of genes.

### 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

    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

    ## 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)

[Package monocle version 2.22.0 Index]