Produce a PCA plot of the data from a GRN object

plotPCA_all(
  GRN,
  outputFolder = NULL,
  basenameOutput = NULL,
  data = c("rna", "peaks"),
  topn = c(500, 1000, 5000),
  type = "normalized",
  removeFiltered = TRUE,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height = 12,
  pages = NULL,
  forceRerun = FALSE
)

Arguments

GRN

Object of class GRN

outputFolder

Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in initializeGRN will be used. Otherwise, all output from this function will be put into the specified folder. If a folder is provided, while we recommend specifying an absolute path, a relative one also works.

basenameOutput

NULL or character. Default NULL. Basename of the output files that are produced. If set to NULL, a default basename is chosen. If a custom basename is specified, all output files will have the chosen basename as file prefix, be careful with not overwriting already existing files (if forceRerun is set to TRUE)

data

Character. Either "peaks" or "rna" or "all". Default c("rna", "peaks"). Type of data to plot a PCA for. "peaks" corresponds to the the open chromatin data, while "rna" refers to the RNA-seq counts. If set to "all", PCA will be done for both data modalities. In any case, PCA will be based on the original provided data before any additional normalization has been run (i.e., usually the raw data).

topn

Integer vector. Default c(500,1000,5000). Number of top variable features to do PCA for. Can be a vector of different numbers (see default).

type

Character. Must be "normalized". On which data type (raw or normalized) should the PCA plots be done? We removed support for raw and currently only support normalized.

removeFiltered

Logical. TRUE or FALSE. Default TRUE. Should features marked as filtered as determined by filterData be removed?

plotAsPDF

TRUE or FALSE. Default TRUE.Should the plots be printed to a PDF file? If set to TRUE, a PDF file is generated, the name of which depends on the value of basenameOutput. If set to FALSE, all plots are printed to the currently active device. Note that most functions print more than one plot, which means you may only see the last plot depending on your active graphics device.

pdf_width

Number>0. Default 12. Width of the PDF, in cm.

pdf_height

Number >0. Default 12. Height of the PDF, in cm.

pages

Integer vector or NULL. Default NULL. Page number(s) to plot. Can be used to plot only specific pages to a PDF or the currently active graphics device.

forceRerun

TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

An updated GRN object with the data of the screeplot and PCA stored in GRN@stats$PCA. Already existing slots are overwritten.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> INFO [2024-06-03 19:59:43] Storing GRN@data$RNA$counts matrix as sparse matrix because fraction of 0s is > 0.1 (0.44)
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
GRN = plotPCA_all(GRN, topn = 500, data = "rna", type = "normalized", plotAsPDF = FALSE, pages = 1)
#> INFO [2024-06-03 19:59:43] Plotting PCA and metadata correlation of normalized RNA data for all shared samples. This may take a few minutes
#> INFO [2024-06-03 19:59:43] Prepare PCA. Count transformation: none
#> INFO [2024-06-03 19:59:43] Plotting directly

#> INFO [2024-06-03 19:59:45] Finished successfully. Execution time: 2.1 secs