ViolinEnsemble: ViolinEnsemble

Description Usage Arguments

View source: R/ViolinEnsemble.R

Description

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

Usage

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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 Nov. 19, 2019, 2:45 a.m.