hippo_feature_heatmap: HIPPO's feature heatmap

In tk382/HIPPO: Heterogeneity-Induced Pre-Processing tOol

Description

HIPPO's feature heatmap

Usage

hippo_feature_heatmap(
  sce,
  switch_to_hgnc = FALSE,
  ref = NA,
  top.n = 50,
  kk = 2,
  plottitle = ""
)

Arguments

sce	SingleCellExperiment object with hippo
switch_to_hgnc	if the current gene names are ensemble ids, and would like to switch to hgnc
ref	a data frame with columns 'hgnc' and 'ensg' to match each other, only required when switch_to_hgnc is set to TRUE
top.n	number of markers to return
kk	integer for the round of clustering that you'd like to see result. Default is 2
plottitle	title for the plot

Value

list of differential expression result

Examples

data(toydata)
set.seed(20200505)
toydata = hippo(toydata,
          feature_method = "zero_inflation",
          clustering_method = "kmeans",
          K = 4,
          outlier_proportion = 0.00001)
hippo_feature_heatmap(toydata)

tk382/HIPPO documentation built on Aug. 17, 2021, 2:29 p.m.