Tutorial R code broken

[ndaniel]

The following R code from the SPATA2 tutorial -- Copy Number Variations (CNV) https://themilolab.github.io/SPATA2/articles/cnv.html

# load required packages
library(SPATA2)
library(SPATAData)
library(tidyverse)

# load SPATA2 object
object_t269 <- downloadSpataObject(sample_name = "UKF269T")

# alternatively, use diet version (results might differ slightly)
object_t269 <- loadExampleObject(sample_name = "UKF269T")

# only histology
plotSurface(object, = object_t269, pt_alpha = 0)

# histological grouping
plotSurface(object = object_t269, color_by = "histology")

shows this error

Error in `dplyr::select()`:
ℹ In argument: `dplyr::all_of(vars)`.
Caused by error in `dplyr::all_of()`:
! Can't subset elements that don't exist.
✖ Element `histology` doesn't exist.

due to missing the histology annotation.
Also there is a typo object, = object_t269 should be object = object_t269.

Running this:

library(SPATA2)
library(tidyverse)

obj <- loadExampleObject("UKF269T", process = TRUE, meta = TRUE)
getSpatAnnIds(obj)

shows this

character(0)