iSEEmarker

iSEEmarker() creates an initial state of an iSEE instance for interactive exploration of marker genes through the DynamicMarkerTable panel, synchronizing selections with a ReducedDimensionPlot and a FeatureAssayPlot to visualize the expression of selected marker genes

Usage

iSEEmarker(
  sce,
  reddim_type = "TSNE",
  clusters = colnames(colData(sce))[1],
  groups = colnames(colData(sce))[1],
  selection_plot_format = c("ColumnDataPlot", "ReducedDimensionPlot")
)

Arguments

sce

SingleCellExperiment object

reddim_type

A string vector containing the dimensionality reduction

clusters

A character string containing the name of the clusters/cell-type/state...(as listed in the colData of the sce)

groups

A character string of the groups/conditions...(as it appears in the colData of the sce)

selection_plot_format

A string character containing the class of the panel. It can be either ColumnDataPlot or ReducedDimensionPlot

Value

A list of "Panel" objects specifying the initial state of iSEE instance

Examples

sce <- scRNAseq::RichardTCellData()
#> snapshotDate(): 2024-10-04
#> loading from cache
sce <- scuttle::logNormCounts(sce)
sce <- scater::runPCA(sce)
sce <- scater::runTSNE(sce)
cluster <- "stimulus"
group <- "single cell quality"
initial <- iSEEmarker(sce = sce, clusters = cluster, groups = group,
selection_plot_format = "ColumnDataPlot")