jackstrawPlot

identify significant prinicipal components (PCs)

jackstrawPlot(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  reduction = c("cells", "feats"),
  feats_to_use = NULL,
  center = FALSE,
  scale_unit = FALSE,
  ncp = 20,
  ylim = c(0, 1),
  iter = 10,
  threshold = 0.01,
  verbose = TRUE,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "jackstrawPlot"
)

Arguments

gobject

giotto object

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

expression_values

expression values to use

reduction

cells or genes

feats_to_use

subset of features to use for PCA

center

center data before PCA

scale_unit

scale features before PCA

ncp

number of principal components to calculate

ylim

y-axis limits on jackstraw plot

iter

number of interations for jackstraw

threshold

p-value threshold to call a PC significant

verbose

show progress of jackstraw method

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

Value

ggplot object for jackstraw method

Details

The Jackstraw method uses the permutationPA function. By systematically permuting genes it identifies robust, and thus significant, PCs.

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> 
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

jackstrawPlot(gobject = g)
#> Error: package 'jackstraw' is not yet installed
#> 
#>  To install:
#> install.packages(c("jackstraw"))