How to create a Giotto object?

1. Minimum requirements

• expression matrix
  
• spatial locations

library(Giotto)

# 1. directly from the file paths
path_to_matrix = system.file("extdata", "seqfish_field_expr.txt", package = 'Giotto')
path_to_locations = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto')

my_giotto_object = createGiottoObject(raw_exprs = path_to_matrix,
                                      spatial_locs = path_to_locations)


# 2. use an existing matrix and data.table
expression_matrix = readExprMatrix(path_to_matrix) # fast method to read expression matrix
cell_locations = data.table::fread(path_to_locations)

my_giotto_object = createGiottoObject(raw_exprs = expression_matrix,
                                      spatial_locs = cell_locations)

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2. Additional features

Previous obtained information can be provided using any of the functions parameters to:
- Add cell or gene metadata
- add spatial networks or grids
- add dimensions reduction
- add giotto images
- add offset file
- add instructions

Usually specificying your own instructions can be most usefull to:
- specify a python path
- determine output of plots
- automatically save plots to selected directory

library(Giotto)

# 1. directly use a path
path_to_matrix = system.file("extdata", "seqfish_field_expr.txt", package = 'Giotto')
path_to_locations = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto')

# 2. create your own instructions
path_to_python = '/usr/bin/python3' # can be something else 
working_directory = getwd() # this will use your current working directory
my_instructions = createGiottoInstructions(python_path = path_to_python,
                                           save_dir = working_directory)

# 3. create your giotto object
my_giotto_object = createGiottoObject(raw_exprs = path_to_matrix,
                                      spatial_locs = path_to_locations,
                                      cell_metadata = my_cell_metadata,
                                      gene_metadata = my_gene_metadata,
                                      instructions = my_instructions)

# 4. check which giotto instructions are associated with your giotto object
showGiottoInstructions(my_giotto_object)