signPCA#

View Source Code

Last Updated: Mar 11, 2023

Description#

identify significant prinicipal components (PCs)

Usage#

signPCA(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  name = NULL,
  method = c("screeplot", "jackstraw"),
  expression_values = c("normalized", "scaled", "custom"),
  reduction = c("cells", "feats"),
  pca_method = c("irlba", "factominer"),
  rev = FALSE,
  feats_to_use = NULL,
  genes_to_use = NULL,
  center = T,
  scale_unit = T,
  ncp = 50,
  scree_ylim = c(0, 10),
  jack_iter = 10,
  jack_threshold = 0.01,
  jack_ylim = c(0, 1),
  verbose = TRUE,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "signPCA"
)

Arguments#

gobject

giotto object

feat_type

feature type

spat_unit

spatial unit

name

name of PCA object if available

method

method to use to identify significant PCs

expression_values

expression values to use

reduction

cells or genes

pca_method

which implementation to use

rev

do a reverse PCA

feats_to_use

subset of features to use for PCA

genes_to_use

deprecated, use feats_to_use

center

center data before PCA

scale_unit

scale features before PCA

ncp

number of principal components to calculate

scree_ylim

y-axis limits on scree plot

jack_iter

number of interations for jackstraw

jack_threshold

p-value threshold to call a PC significant

jack_ylim

y-axis limits on jackstraw plot

verbose

verbosity

show_plot

show plot

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters from all_plots_save_function()

default_save_name

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

Details#

Two different methods can be used to assess the number of relevant or significant prinicipal components (PC’s).
1. Screeplot works by plotting the explained variance of each individual PC in a barplot allowing you to identify which PC provides a significant contribution (a.k.a. ‘elbow method’).
2. The Jackstraw method uses the permutationPA function. By systematically permuting genes it identifies robust, and thus significant, PCs.

Value#

ggplot object for scree method and maxtrix of p-values for jackstraw