zero_proportion_plot {HIPPO}R Documentation

visualize each round of hippo through zero proportion plot

Description

visualize each round of hippo through zero proportion plot

Usage

zero_proportion_plot(
  sce,
  switch_to_hgnc = FALSE,
  ref = NA,
  k = NA,
  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

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(20200321)
toydata = hippo(toydata,K = 10,z_threshold = 1,outlier_proportion = 0.01)
data(ensg_hgnc)
zero_proportion_plot(toydata, switch_to_hgnc = TRUE, ref = ensg_hgnc)

[Package HIPPO version 1.4.0 Index]