get_violin_data: Get data for single-cell violin plots

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

Get data for single-cell violin plots

Description

Get data for single-cell violin plots

Usage

get_violin_data(
  feature,
  scseq,
  selected_cluster,
  by.sample = FALSE,
  decreasing = feature %in% c("ribo_percent", "log10_sum", "log10_detected"),
  with_all = FALSE,
  h5logs = NULL
)

Arguments

feature	Feature name to generate violin plot for. Either a row or colData of scseq.
scseq	SingleCellExperiment.
selected_cluster	Name of the selected cluster.
by.sample	if TRUE plot feature violin for each scseq$batch. Default (FALSE) will plot feature for each scseq$cluster.
decreasing	if TRUE, violinlines with smaller mean values of feature will show up on top. Used to show features where smaller values indicate potential QC issues.
with.height	Whether to return height of plot. See value for details.

Value

list used by VlnPlot

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