plot_pathway_dendrogram: Plot pathway dendrogram

Description Usage Arguments Value Examples

View source: R/plot_pathway_dendrogram.R

Description

plot_pathway_dendrogram() plots the results of output from the fgsea() function.

Usage

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plot_pathway_dendrogram(path_res_df, cluster = "col",
  clustering_distance = "euclidean", clustering_method = "complete",
  flip_dendro = F)

Arguments

path_res_df

dataframe should contain columns "CellType", "pathway", "NES";can be output from the fgsea() function

cluster

what to cluster; possible values are "pathway" or "CellType"

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 for clustering. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).

flip_dendro

logical; if dendrogram should be flipped

Value

A ggplot2 object

Examples

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plot_pathway_dendrogram(path_res_df=my_pathway_enrichment)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.