In FridleyLab/spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

knitr::opts_chunk$set(
  collapse=TRUE,
  comment="#>",
  fig.width=10, fig.height=7
)
options(rmarkdown.html_vignette.check_title=F)

When installing spatialGE, I get Error in utils::download.file(url, path, method = method, quiet = quiet. How can I solve this error?

This error might appear when installing spatialGE:

Downloading GitHub repo FridleyLab/spatialGE@oospina_dev
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/FridleyLab/spatialGE/tarball/oospina_dev' failed

A workaround is to set options(timeout) to a large number:

options(timeout=9999999) # To avoid R closing connection with GitHub
devtools::install_github("fridleylab/spatialGE")

The gene_interpolation function outputs an error: Error in solve.default(qr.R(qr.VT)). What can be done about it?

When running the gene_interpolation function with REML=TRUE, you may get this error:

Error in solve.default(qr.R(qr.VT)) : 
  Lapack routine dgesv: system is exactly singular: U[1,1] = 0
Error in call to optim
spatialProcess: Problems with optim in mKrigMLEJoint 
returned object includes the likelihood evaluations up to the error

This error occurs during REML parameter estimation, and it means that the gene expression surface estimated might not be accurate. Nonetheless, if you run the STplot_interpolation on the STlist resulting from gene_interpolation, you will notice that gene expression surfaces have actually been generated for the other genes and samples despite the error being presented.

If you still want to obtain gene expression surfaces for the other genes for which gene_interpolation could not produce a surface, you can try REML=F, which is a slower procedure.

When using readRDS to load an STList, I get ‘Error: vector memory exhausted’. What can I do?

This error results from R’s default memoery limits. Provided your computer has enough memory to hold an STList in memory, this error message can be overridden by typing in a Terminal (Mac OS):

echo 'R_MAX_VSIZE=100Gb' >> ~/.Renviron

Then, close and re-open R and try to load the STList again.

FridleyLab/spatialGE documentation built on April 14, 2025, 9:37 a.m.