plot_densities: Plot sample-specific densities.

In distinct: distinct: a method for differential analyses via hierarchical permutation tests

Description

plot_densities returns a ggplot object with the sample-specific density estimates, for a specified cluster and gene.

Usage

plot_densities(
  x,
  name_assays_expression = "logcounts",
  name_cluster = "cluster_id",
  name_sample = "sample_id",
  name_group = "group_id",
  cluster,
  gene,
  group_level = FALSE
)

Arguments

x	a SummarizedExperiment or a SingleCellExperiment object.
name_assays_expression	a character ("logcounts" by default), indicating the name of the assays(x) element which stores the expression data (i.e., assays(x)$name_assays_expression). We strongly encourage using normalized data, such as counts per million (CPM) or log-CPM.
name_cluster	a character ("cluster_id" by default), indicating the name of the colData(x) element which stores the cluster id of each cell (i.e., colData(x)$name_colData_cluster).
name_sample	a character ("sample_id" by default), indicating the name of the colData(x) element which stores the sample id of each cell (i.e., colData(x)$name_colData_sample).
name_group	a character ("group_id" by default), indicating the name of the colData(x) element which stores the group id of each cell (i.e., colData(x)$name_colData_group).
cluster	a character, indicating the name of the cluster to plot.
gene	a character, indicating the name of the gene to plot.
group_level	a logical, indicating whether to plot group-level (if TRUE) or sample-level curves (if FALSE).

Value

A ggplot object.

Author(s)

Simone Tiberi [e-mail]

See Also

distinct_test, plot_cdfs

Examples

data("Kang_subset", package = "distinct")
Kang_subset

plot_densities(x = Kang_subset,
               gene = "ISG15",
               cluster = "Dendritic cells",
               name_assays_expression = "logcounts",
               name_cluster = "cell",
               name_sample = "sample_id",
               name_group = "stim")

distinct documentation built on Nov. 8, 2020, 8:20 p.m.