Join giotto objects#
Last Updated: Sep 07, 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#
|
list of giotto objects |
|
unique giotto names for each giotto object |
|
method to join giotto objects, see details |
|
distance(s) along z-axis if method is z-stack (default is step of 1000) |
|
list of values to shift along x-axis if method is shift |
|
list of values to shift along y-axis if method is shift |
|
padding between datasets/images if method is shift |
|
padding between datasets/images if method is shift |
|
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
, andy_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
andy_padding
. Both shift and padding values can be used at the same time.Leaving
x_shift
andy_shift
values asNULL
will have Giotto estimate an appropriatex_shift
value based on the x dimension of available image objects. If no image objects are available, a default behavior ofx_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 ingobject_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