bb_gene_violinplot: Make a plot of gene expression in UMAP form
In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

bb_gene_violinplot

R Documentation

Make a plot of gene expression in UMAP form

Description

Make a plot of gene expression in UMAP form

Usage

bb_gene_violinplot(
  cds,
  variable,
  genes_to_plot,
  experiment_type = "Gene Expression",
  pseudocount = 1,
  include_jitter = FALSE,
  ytitle = "Expression",
  plot_title = NULL,
  rows = 1,
  show_x_label = TRUE,
  legend_pos = "none",
  comparison_list = NULL,
  palette = NULL,
  violin_alpha = 1,
  jitter_alpha = 1,
  jitter_color = "black",
  jitter_fill = "transparent",
  jitter_size = 0.5,
  facet_scales = "fixed",
  order_genes = TRUE,
  jitter_match = FALSE,
  rasterize = FALSE,
  raster_dpi = 300
)

Arguments

`cds`	A cell data set object
`variable`	Stratification variable for x-axis
`genes_to_plot`	Either a character vector of gene short names or a tbl/df where the first column is gene short name and the second is the gene grouping.
`pseudocount`	Value to add to zero-cells
`include_jitter`	Include jitter points
`ytitle`	Title for y axis
`plot_title`	Main title for the plot
`rows`	Number of rows for facetting
`show_x_label`	Option to show x label
`legend_pos`	Position for label
`comparison_list`	Optional list of comparisons for ggpubr
`palette`	Color palette to use. Viridis is default.
`violin_alpha`	Alpha value for violin plot
`jitter_alpha`	Alpha value for jitter plot
`jitter_color`	Color for the jitter plot. Defaults to black and ignored if jitter_match == TRUE
`jitter_fill`	Fill for the jitter plot
`jitter_size`	Size of the jitter points
`facet_scales`	Scale option for facetting. "Fixed" is default
`order_genes`	If true, put genes in the same order as variable parameter
`jitter_match`	If true, match jitter color to violin fill.
`rasterize`	Whether to render the graphical layer as a raster image. Default is FALSE.
`raster_dpi`	If rasterize then this is the DPI used. Default = 300.