Installation#

Date:

4/12/23

1 Installing Giotto Suite#

Giotto Suite is installed via R but there are required Python modules which must be installed in order for Giotto Suite to function properly. Below are the instructions for both the installation of the Giotto Suite package and required Python environment.

1.1 Requirements#

  • R (>= 4.0.1)

  • Python (>= 3.6)

  • Windows, MacOS or Linux specific installation tools for Posit (previously RStudio)

2 Installation#

2.1 Install Giotto Suite#

# Necessary for installation from R
if(!"devtools" %in% installed.packages()) {
  install.packages("devtools")
}

devtools::install_github("drieslab/Giotto@suite")

2.2 Install the Giotto Python Environment#

library(Giotto)
installGiottoEnvironment()

3 Try Giotto in the cloud#

You can also run analyses in Giotto on Terra.bio. Take a look on the Terra tutorial.

Encountering errors? Checkout out the Troubleshooting page for help. Alternatively, post to an issue to the Giotto GitHub page here. Please include the version numbers of R, Giotto, and the OS in use at the time of the issue.

4 Session Info#

sessionInfo()

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Giotto_3.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10       pillar_1.9.0      compiler_4.2.2    tools_4.2.2
 [5] digest_0.6.30     jsonlite_1.8.3    evaluate_0.20     lifecycle_1.0.3
 [9] tibble_3.2.1      gtable_0.3.3      lattice_0.20-45   pkgconfig_2.0.3
[13] rlang_1.1.0       Matrix_1.5-1      cli_3.4.1         rstudioapi_0.14
[17] parallel_4.2.2    yaml_2.3.7        xfun_0.38         fastmap_1.1.0
[21] terra_1.7-18      dplyr_1.1.1       knitr_1.42        generics_0.1.3
[25] vctrs_0.6.1       grid_4.2.2        tidyselect_1.2.0  glue_1.6.2
[29] data.table_1.14.6 R6_2.5.1          fansi_1.0.4       rmarkdown_2.21
[33] ggplot2_3.4.1     magrittr_2.0.3    scales_1.2.1      codetools_0.2-18
[37] htmltools_0.5.4   colorspace_2.1-0  utf8_1.2.3        munsell_0.5.0