Skip to contents

Load and parse data, csv

make_count_data_csv.Rd

Loads MERFISH data from a csv file, or multiple files in a directory, and combines them into a single data frame. This function was written for "in house" use by Michael Barkasi, and was not intended for general use. You can try it, but it may not work for your data and isn't documented in a user-friendly way.

Usage

make_count_data_csv(
  data_path,
  remove_L1 = TRUE,
  initialize_zeros = FALSE,
  load_first_file_only = FALSE,
  verbose = TRUE
)

Arguments

data_path

Path to the directory containing the HDF5 files@aliases

remove_L1

Logical, whether to exclude cells in layer 1 (default is TRUE)

initialize_zeros

Logical, whether to initialize new coordinate columns to zero (default is FALSE)

load_first_file_only

Logical, whether to load only the first file found (default is FALSE)

verbose

Logical, whether to print progress messages (default is TRUE)

Value

A list containing the combined count data and a list of slice plots for each mouse