Initiate an object of class SPATA2 from platform MERFISH

This function initiates a SPATA2 object with data generated using the MERFISH platform.

initiateSpataObjectMERFISH(
  sample_name,
  directory_merfish,
  read_transcripts = FALSE,
  file_counts = NULL,
  file_cell_meta = NULL,
  file_transcripts = NULL,
  verbose = TRUE
)

Arguments

directory_merfish

Character value. Directory to a MERFISH folder that should contain a .csv file called ~/...cell_by_gene.csv and a .csv file called ~/...cell_metadata.csv, where ~ is the directory to the folder. Deviating filenames can be specified using arguments file_counts and file_cell_meta, respectively.

read_transcripts

Logical value. If TRUE, the actual transcript positions are read in via ~/...detected_transcript.csv or the input of file_transcripts, if specified. Note that this argument defaults to FALSE since reading file transcripts can increase the object size by several GB.

file_counts

Character value or NULL. If character, specifies the filename of .csv file that contains the gene counts by cell. Use only if filename deviates from the default.

file_cell_meta

Character value or NULL. If character, specifies the filename of the .csv file that contains cell meta data, in particular, spatial location via the variables center_x and center_y.

file_transcripts

Character value or NULL. If character, specifies the filename of the .csv file that contains molecule transcript positions, in particular, spatial location via the variables x and y.

verbose

Logical. If TRUE, informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

Value

A SPATA2 object from the MERFISH platform. Default for pt_size is set to 0.4 which might need adjustment.

Details

MERFISH works in micron space. The coordinates of the cellular centroids are provided in unit um. Therefore no pixel scale factor must be computed or set to work with SI units.