Iterate_Barcode_Rank_Plot {scCustomize} | R Documentation |
Iterative Barcode Rank Plots
Description
Read data, calculate DropletUtils::barcodeRanks
, create barcode rank plots, and outout single PDF output.
Usage
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 |
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 |
cellranger_multi |
logical, whether the outputs to be read are from Cell Ranger |
parallel |
logical, should files be read in parallel (default is FALSE). |
num_cores |
Number of cores to use in parallel if |
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 |
Value
pdf document
Examples
## Not run:
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")
## End(Not run)