bubbleplot: bubbleplot

In milescsmith/bubbleplot: Create bubble plot of scRNAseq expression data from Seurat

Description

Display percentage of cells expressing and levels for a set of features.

Usage

bubbleplot(object, ...)

## S3 method for class 'Seurat'
bubbleplot(
  object,
  features_plot,
  assay = NULL,
  slot = "data",
  filter_exp_pct = NULL,
  filter_apply_method = "any",
  filter_apply_group = NULL,
  filter_exp_pct_thresh = 0,
  filter_exp_level = 0,
  avg_func = "mean",
  grouping_var = "ident",
  x_lab_size = 9,
  y_lab_size = 9,
  x_axis_title = "Features",
  y_axis_title = "Grouping",
  pct_legend_title = "Percent group expressing",
  scale_legend_title = "Average scaled expression",
  x_lab_rot_angle = 45,
  preserve_feature_order = FALSE,
  cluster_x = TRUE,
  cluster_y = FALSE,
  colors_use = NULL,
  translate_feature_names = FALSE,
  annotated_feature_list = FALSE,
  do_return = FALSE,
  verbose = FALSE,
  ...
)

Arguments

object	Seurat object
...	ignored
features_plot	Either a list of features or a data frame of annotated features to display (see 'annotated_feature_list'). Note: Gene and protein names may be converted to the proper feature name automagically by HGNChelper::checkGeneSymbols if 'translate_feature_names' is TRUE. Features not appearing in the dataset are skipped.
assay	Assay to plot. Default: "RNA"
slot	Slot to plot. Default: "data"
filter_exp_pct	Display only features that are expressed above this fraction. The method by which and groups in which this is judged are controlled by 'filter_apply_method' and 'filter_apply_group', respectively. Default: NULL
filter_apply_method	How should 'filter_exp_pct' be applied - should 'any' or 'all' groups be above the desired expression level? Default: "any"
filter_apply_group	What identity groups should be considered when applying 'filter_exp_pct? Only works with the active identity or whatever is specified in 'grouping_var'. Default: NULL
filter_exp_pct_thresh	Threshold for expression fraction. Default: 0
filter_exp_level	Display only features that are expressed above this level in at least one group. Default: 0
avg_func	Base function to call for measuring average expression. Default: "mean"
grouping_var	Variable by which to group cells. Can be cluster identities or any column from the meta.data slot. Default: ident
x_lab_size	Font size for the x-axis labels. Default: 9
y_lab_size	Font size for the y-axis labels. Default: 9
x_axis_title	x-axis title
y_axis_title	y-axis title
pct_legend_title	Percent expressed legend title
scale_legend_title	Scale legend title.
x_lab_rot_angle	Angle to rotate the x-axis labels. Default: 45°
preserve_feature_order	Should the features by displayed in order in which they are given? Overrides cluster_x. Default: FALSE.
cluster_x	Arrange the x-axis variables using hierarchical clustering. Default: TRUE
cluster_y	Arrange the y-axis variables using hierarchical clustering. Default: FALSE
colors_use	Color palette to use to display expression levels. Default: "Reds"
translate_feature_names	Should feature names be checked and translated to their correct HUGO Gene Nomenclature Committee name? Default: FALSE
annotated_feature_list	Is the feature list annotated? If so, the features will be faceted using their annontations. Requires that 'features_plot' is a two column with the annotations in a column named 'annotations' and features in a column named 'features'. Default: FALSE
do_return	Return a ggplot2 object instead of displaying
verbose	Show extra output information, like the features that were not found? Default: FALSE

Value

if isTRUE(do_return), a ggplot2 object

milescsmith/bubbleplot documentation built on Jan. 22, 2022, 3:10 p.m.