joinGiottoObjects: Join giotto objects
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

joinGiottoObjects

R Documentation

Join giotto objects

Description

Function to join multiple giotto objects together

Usage

joinGiottoObjects(
  gobject_list,
  gobject_names = NULL,
  join_method = c("shift", "z_stack", "no_change"),
  z_vals = 1000,
  x_shift = NULL,
  y_shift = NULL,
  x_padding = NULL,
  y_padding = NULL,
  verbose = TRUE
)

Arguments

`gobject_list`	list of giotto objects
`gobject_names`	unique giotto names for each giotto object
`join_method`	method to join giotto objects, see details
`z_vals`	distance(s) along z-axis if method is z-stack (default is step of 1000)
`x_shift`	list of values to shift along x-axis if method is shift
`y_shift`	list of values to shift along y-axis if method is shift
`x_padding`	padding between datasets/images if method is shift
`y_padding`	padding between datasets/images if method is shift
`verbose`	be verbose Preview where each gobject will be in space with bounding polygons

Details

This function joins both the expression and spatial information of multiple giotto objects into a single one. Giotto supports multiple ways of joining spatial information as selected through param join_method:

"shift" (default) Spatial locations of different datasets are shifted by numeric vectors of values supplied through x_shift, y_shift, x_padding, and y_padding. This is particularly useful for data that is provided as tiles or ROIs or when analyzing multiple spatial datasets together and keeping their spatial data separate.

If shift values are given then a value is needed for each giotto object to be joined in gobject_list. Order matters.

If a regular step value is desired instead of a specific list of values, use x_padding and y_padding. Both shift and padding values can be used at the same time.

Leaving x_shift and y_shift values as NULL will have Giotto estimate an appropriate x_shift value based on the x dimension of available image objects. If no image objects are available, a default behavior of x_padding = 1000 will be applied.
"z_stack" Datasets are spatially combined with no change to x and y spatial locations, but a z value is incorporated for each dataset based on input supplied through param z_vals. To specify a z value for each dataset to join, a numeric vector must be given with a value for each element in gobject_list. Order matters.

Alternatively, a single numeric value can be supplied to z_vals in which case this input will be treated as a z step value.
"no_change" No changes are applied to the spatial locations of the datasets when joining.