plot_violin: Violin Plot

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Violin Plot

Description

Violin Plot

Usage

plot_violin(
  feature = NULL,
  scseq = NULL,
  selected_cluster = NULL,
  by.sample = FALSE,
  with_all = FALSE,
  with.height = FALSE,
  violin_data = NULL,
  is_mobile = FALSE,
  hide_pct = is_mobile,
  hide_ncells = is_mobile,
  decreasing = feature %in% c("ribo_percent", "log10_sum", "log10_detected")
)

Arguments

feature	Character, gene name.
scseq	SingleCellExperiment object.
selected_cluster	Integer indicating which level(scseq$cluster) to highlight (if by.sample is FALSE) or to subset data to (if by.sample is TRUE). To plot by sample without subsetting to a cluster, set to nlevels(scseq$cluster) + 1.
by.sample	Boolean indicating if violin plots should be by sample or by cluster (default).
with_all	Set to TRUE if plotting by sample to get same colors as Shiny app.
with.height	if TRUE returns a list object with plot and appropriate height.
violin_data	Used for Shiny app. Result of get_violin_data. Used when logcounts are seperate from SingleCellExperiment as in the Shiny app.
is_mobile	If TRUE shortens up y-axis labels to fit mobile better.
hide_pct	If TRUE, barplots indicating number of cells are hidden.
hide_ncells	If TRUE, barplots indicating percent expression are hidden.
decreasing	if FALSE (default) violins are ordered, bottom to top, by increasing mean expression.

Value

ggplot or list

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.