Join giotto objects#

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Last Updated: Mar 11, 2023

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.

Value#

giotto object