ViolinEnsemble: ViolinEnsemble

In milescsmith/ViolinEnsemble: Create violin plots of gene expression for multiple genes

Description

Produce grouped violin plots. Suitable for plotting cluster or cell type specific marker features.

Usage

ViolinEnsemble(
  object,
  features = NULL,
  marker_list = NULL,
  grouping_var = NULL,
  make_features_unique = TRUE,
  cluster_x = FALSE,
  cluster_y = FALSE,
  show_points = FALSE,
  alpha = 0.5,
  pt_size = 0.25,
  plot_title = NULL,
  assay_use = "RNA",
  slot_use = "data",
  sort = FALSE,
  flip = TRUE
)

Arguments

object	Seurat object to plot
features	List of features to plot
marker_list	A table of cluster markers as produced by FindMarkers() or FindAllMarkers or a two column data.frame with the columns "cluster" and "feature". If provided, supercedes the features argument. Note: if a marker is present in multiple clusters, only the first (as determined by arrange()) is used. Default: NULL
grouping_var	Grouping variable from ident or meta data to use. If NULL, the current active.ident is used. Default: NULL
make_features_unique	For a marker list, keep a feature for only the first cluster it is found it.
cluster_x	Arrange the x-axis variables using hierarchical clustering. Default: TRUE
cluster_y	Arrange the y-axis variables using hierarchical clustering. Default: FALSE
show_points	Display data points in addition to violin using geom_jitter? Default: FALSE
alpha	Alpha value to use with geom_jitter. Default: 1
pt_size	Point size to use with geom_jitter. Default: 0.25
plot_title	What it says on the tin. Default: NULL
assay_use	Assay to plot. Default: "RNA"
slot_use	Slot to draw data from. Default: "data"
sort	If TRUE, attempt to sort the groups alpha-numerically. Default: FALSE
flip	Should features be displayed along the y-axis? Default: TRUE

milescsmith/ViolinEnsemble documentation built on Feb. 14, 2020, 9:15 a.m.