vignettes/tut1_giotto_object.Rmd
tut1_giotto_object.Rmdlibrary(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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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)