warning_plot_reduced_dim_scExp: A warning helper for plot_reduced_dim_scExp

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

A warning helper for plot_reduced_dim_scExp

Description

A warning helper for plot_reduced_dim_scExp

Usage

warning_plot_reduced_dim_scExp(
  scExp,
  color_by,
  reduced_dim,
  downsample,
  transparency,
  size,
  max_distanceToTSS,
  annotate_clusters,
  min_quantile,
  max_quantile
)

Arguments

scExp	A SingleCellExperiment Object
color_by	Feature used for coloration
reduced_dim	Reduced Dimension used for plotting
downsample	Number of cells to downsample
transparency	Alpha parameter, between 0 and 1
size	Size of the points.
max_distanceToTSS	Numeric. Maximum distance to a gene's TSS to consider a region linked to a gene.
annotate_clusters	A logical indicating if clusters should be labelled. The 'cell_cluster' column should be present in metadata.
min_quantile	The lower threshold to remove outlier cells, as quantile of cell embeddings (between 0 and 0.5).
max_quantile	The upper threshold to remove outlier cells, as quantile of cell embeddings (between 0.5 and 1).

Value

Warning or errors if the inputs are not correct

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.