Create a Giotto Object

createGiottoObject()

Function to create a Giotto Object.

createGiottoObject(
    raw_exprs,
    spatial_locs = NULL,
    norm_expr = NULL,
    norm_scaled_expr = NULL,
    custom_expr = NULL,
    cell_metadata = NULL,
    gene_metadata = NULL,
    spatial_network = NULL,
    spatial_network_name = NULL,
    spatial_grid = NULL,
    spatial_grid_name = NULL,
    spatial_enrichment = NULL,
    spatial_enrichment_name = NULL,
    dimension_reduction = NULL,
    nn_network = NULL,
    images = NULL,
    offset_file = NULL,
    instructions = NULL,
    cores = NA
)

Arguements

raw_exprs	matrix with raw expression counts [required]
spatial_locs	data.table or data.frame with coordinates for cell centroids
norm_expr	normalized expression values
norm_scaled_expr	scaled expression values
custom_expr	custom expression values
cell_metadata	cell annotation metadata
gene_metadata	gene annotation metadata
spatial_network	list of spatial network(s)
spatial_network_name	list of spatial network name(s)
spatial_grid	list of spatial grid(s)
spatial_grid_name	list of spatial grid name(s)
spatial_enrichment	list of spatial enrichment score(s) for each spatial region
spatial_enrichment_name	list of spatial enrichment name(s)
dimension_reduction	list of dimension reduction(s)
nn_network	list of nearest neighbor network(s)
images	list of images
offset_file	file used to stitch fields together (optional)
instructions	list of instructions or output result from createGiottoInstructions
cores	how many cores or threads to use to read data if paths are provided

Value

Giotto Object

Details

[Requirements] To create a giotto object you need to provide at least a matrix with genes as row names and cells as column names. This matrix can be provided as a base matrix, sparse Matrix, data.frame, data.table or as a path to any of those. To include spatial information about cells (or regions) you need to provide a matrix, data.table or data.frame (or path to them) with coordinates for all spatial dimensions. This can be 2D (x and y) or 3D (x, y, x). The row order for the cell coordinates should be the same as the column order for the provided expression data.

[Instructions] Additionally an instruction file, generated manually or with createGiottoInstructions can be provided to instructions, if not a default instruction file will be created for the Giotto object.

[Multiple fields] In case a dataset consists of multiple fields, like seqFISH+ for example, an offset file can be provided to stitch the different fields together. stitchFieldCoordinates can be used to generate such an offset file.

[Processed data] Processed count data, such as normalized data, can be provided using one of the different expression slots (norm_expr, norm_scaled_expr, custom_expr).

[Metadata] Cell and gene metadata can be provided using the cell and gene metadata slots. This data can also be added afterwards using the addGeneMetadata or addCellMetadata functions.

[Other Information] Additional information can be provided through the appropriate slots:

• Spatial networks

• Spatial girds

• Spatial enrichments

• Dimensions reductions

• Nearest neighbours networks

• Images