plot_clusters {monocle} | R Documentation |
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.
plot_clusters( cds, clustering, drawSummary = TRUE, sumFun = mean_cl_boot, ncol = NULL, nrow = NULL, row_samples = NULL, callout_ids = NULL )
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 |
a ggplot2 plot object
## 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)