View source: R/dimension_reduction.R
jackstrawPlot | R Documentation |
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,
genes_to_use = NULL,
center = FALSE,
scale_unit = FALSE,
ncp = 20,
ylim = c(0, 1),
iter = 10,
threshold = 0.01,
verbose = TRUE,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "jackstrawPlot"
)
gobject |
giotto object |
spat_unit |
spatial unit |
feat_type |
feature type |
expression_values |
expression values to use |
reduction |
cells or genes |
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 |
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 |
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 |
The Jackstraw method uses the permutationPA
function. By
systematically permuting genes it identifies robust, and thus significant, PCs.
ggplot object for jackstraw method
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.