zero_proportion_plot: visualize each round of hippo through zero proportion plot

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

Description

visualize each round of hippo through zero proportion plot

Usage

zero_proportion_plot(
  sce,
  switch_to_hgnc = FALSE,
  ref = NA,
  k = NA,
  show_topmarkers = FALSE,
  plottitle = "",
  top.n = 5,
  pointsize = 0.5,
  pointalpha = 0.5,
  textsize = 3
)

Arguments

sce	SingleCellExperiment object with hippo element in it
switch_to_hgnc	boolean argument to indicate whether to change the gene names from ENSG IDs to HGNC symbols
ref	a data frame with hgnc column and ensg column
k	select rounds of clustering that you would like to see result. Default is 1 to K
show_topmarkers	mark the names with the highest zero proportion
plottitle	Title of your plot output
top.n	number of top genes to show the name
pointsize	size of the ggplot point
pointalpha	transparency level of the ggplot point
textsize	text size of the resulting plot

Value

a ggplot object that shows the zero proportions for each round

Examples

data(toydata)
set.seed(20200505)
toydata = hippo(toydata,
          feature_method = "zero_inflation",
          clustering_method = "kmeans",
          K = 4,
          outlier_proportion = 0.00001)
data(ensg_hgnc)
zero_proportion_plot(toydata, switch_to_hgnc = TRUE, ref = ensg_hgnc)

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