plot_CoGAPS_pattern_cor_dendrogram: Plot CoGAPS pattern correlation dendrogram
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

View source: R/plot_CoGAPS_pattern_cor_dendro.R

plot_CoGAPS_pattern_cor_dendro() plots a dendrogram showing the clustering of the correlation of a CoGAPS pattern set with a grouping variable

plot_CoGAPS_pattern_cor_dendrogram(CoGAPS_res_set = NULL, Pattern_set,
  pattern_subset = NULL, annotation, group_column = NULL, group_vector,
  order_subgroups = F, cluster = "patterns",
  clustering_distance = "correlation", clustering_method = "complete")

`CoGAPS_res_set`	a CoGAPS result set. If set to NULL, a Pmeans matrix may be supplied directly as input for the Pattern_set parameter.
`Pattern_set`	a string specifying the name of a pattern set (e.g. "nP20") in a CoGAPS_res_set. Alternatively, if CoGAPS_res_set is set to NULL, a Pmeans matrix may be supplied directly.
`pattern_subset`	a vector specifying a subset of the pattern set to be plotted. Defaults to NULL.
`annotation`	an annotation dataframe. If group_column is set to NULL, must contain logical columns with column names corresponding to values in group_vector. Each logical column (1 or 0) should indicate whether an annotation row is of the value (column name).
`group_column`	column name of column in annotation object with values corresponding to those in group_vector to use for computing logical columns. Defaults to NULL
`group_vector`	a vector of with pre-specified values corresponding to those in group_column in the annotation object.
`order_subgroups`	logical; if subgroups should be ordered according to clustering of first subgroup. Subgroups can be specified in a string with separation by " - ". Only valid if cluster is set to "groups".
`cluster`	what to cluster. Possible values are "patterns" or "groups".
`clustering_distance`	distance measure used in clustering. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)
`clustering_method`	clustering method used. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).

a ggplot object

1
2
3

plot_CoGAPS_pattern_cor_heatmap(CoGAPS_res_set= my_CoGAPS_res, Pattern_set="nP30",  annotation=pData(cds), 
group_column=NULL, group_vector=genotype_vector, order_subgroups=T, cluster= "groups",
clustering_distance = "correlation", clustering_method = "complete")