joinGiottoObjects#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/giotto.R#L3688

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 = 0,
  y_padding = 0,
  verbose = TRUE
)

Arguments#

Argument

Description

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

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? ] Spatial locations of different datasets are shifted by numeric vectors of values supplied through x_shift and y_shift . If these shift values are given then one 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.

[ “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