plot_violin: plot_violin

In garber-lab/VDJChef: VDJChef for vdj analysis

plot_violin

Description

Create violin plot. Function from Garber Lab SignallingSingleCell, modified for input Seurat Object and Expression Set

Usage

plot_violin(
  input,
  title = "",
  gene,
  color_by,
  log_scale = F,
  colors = NULL,
  facet_by = NULL,
  spread = NULL,
  jitter_pts = T,
  plot_mean = T,
  plot_mean_dot_size = 2,
  size = 1,
  sig = 3,
  number_labels = T,
  text_sizes = c(20, 10, 5, 10, 5, 5, 2),
  alpha = 0.5,
  theme = "classic",
  contour_line_width = 0.3
)

Arguments

input	SatijaLab’s Seurat Class, with normalized expression values in assay data slot. Or input Bioconductor’s ExpressionSet Class with (not log) values in exprs().
title	Title of the graph. Would be the gene name if not specified
gene	Feature for which to plot the expression level. For Seurat Object, ensure the correct DefaultAssay is specified prior to running this function. May access gene data through "assayname_GENE" e.g. "rna_CD8A", "adt_CD8"
color_by	a meta.data column variable (Seurat) or pData variable (ExpressionSet).
log_scale	If true, transform UMIs by log2(UMI + 1).
colors	What colors to utilize for categorical data. Be sure it is of the proper length.
facet_by	a vector with one or two meta.data column variables (Seurat) or pData variables (ExpressionSet). If two, the first variable as columns and the second as rows.
spread	e.g. Healthy category is unique in Disease and Skin. To use Healthy only as skin but not Disease, that is adding Healthy skin to each disease, spread = c("Disease", "Healthy").
plot_mean	plot the mean value as black dot with second y-axis on the right.
size	the size of dots.
sig	the number of digits after the decimal point for cell fraction value.
number_labels	show the total cell numbers and cell fraction with non-zero expression values under each bar.
text_sizes	a vector of title_size, axis_title, axis_text, legend_title, legend_text, facet_text, number_label_text_size, defaults too c(20,10,5,10,5,5,2)
theme	the plot theme. Default to be "classic" if not set to "bw".
contour_line_width	the thickness of the violin contour line

Details

Utilize information stored in meta.data to control the plot display. Each point_by as a dot with a bar showing the weighted mean of all point_by dots.

Examples

plot_violin(ex_sc gene = "CD8A", color_by = "Skin", facet_by = c("Disease", "CellType"), log_scale = F)
plot_violin(ex_sc, gene = "adt_CD8", color_by = "Skin", facet_by = c("Disease", "CellType"), log_scale = F)
plot_violin(ex_sc, gene = "CXCL13", color_by = "Skin", facet_by = c("CellType", "Disease"), spread = T, log_scale = T)

garber-lab/VDJChef documentation built on Aug. 30, 2022, 3:30 a.m.