Iterative Barcode Rank Plots — Iterate_Barcode_Rank

Read data, calculate DropletUtils::barcodeRanks, create barcode rank plots, and outout single PDF output.

Iterate_Barcode_Rank_Plot(
  dir_path_h5,
  multi_directory = TRUE,
  h5_filename = "raw_feature_bc_matrix.h5",
  cellranger_multi = FALSE,
  parallel = FALSE,
  num_cores = NULL,
  file_path = NULL,
  file_name = NULL,
  pt.size = 6,
  raster_dpi = c(1024, 1024),
  plateau = NULL,
  ...
)

Arguments

dir_path_h5: path to parent directory (if multi_directory = TRUE) or directory containing all h5 files (if multi_directory = FALSE).
multi_directory: logical, whether or not all h5 files are in their own subdirectories or in a single directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).
h5_filename: Either the file name of h5 file (if multi_directory = TRUE) or the shared suffix (if multi_directory = FALSE)
cellranger_multi: logical, whether the outputs to be read are from Cell Ranger multi as opposed to Cell Ranger count (default is FALSE). Only valid if multi_directory = FALSE.
parallel: logical, should files be read in parallel (default is FALSE).
num_cores: Number of cores to use in parallel if parallel = TRUE.
file_path: file path to use for saving PDF output.
file_name: Name of PDF output file.
pt.size: point size for plotting, default is 6.
raster_dpi: Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(1024, 1024).
plateau: numerical values at which to add vertical line designating estimated empty droplet plateau (default is NULL). Must be vector equal in length to number of samples.
...: Additional parameters passed to Read10X_h5_Multi_Directory or Read10X_h5_GEO.

Value

pdf document

Examples

if (FALSE) {
Iterate_Barcode_Rank_Plot(dir_path_h5 = "H5_PATH/", multi_directory = TRUE,
h5_filename = "raw_feature_bc_matrix", parallel = TRUE, num_cores = 12, file_path = "OUTPUT_PATH",
file_name = "Barcode_Rank_Plots")
}