Skip to content

Commit

Permalink
Merge pull request #858 from josschavezf/suite
Browse files Browse the repository at this point in the history 
update session info website
  • Loading branch information
@josschavezf
josschavezf authored Jan 8, 2024
2 parents 1b80cfc + 850fe88 commit e6a48c6
Show file tree
Hide file tree
Showing 4 changed files with 230 additions and 99 deletions.
2 changes: 1 addition & 1 deletion R/convenience.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2633,7 +2633,7 @@ createArchRProj <- function(fragmentsPath,

if(!requireNamespace('ArchR')) {
wrap_msg('ArchR is needed. Install the package using remotes::install_github("GreenleafLab/ArchR")')
} else {require(ArchR)}
}

## Add reference genome
wrap_msg('Loading reference genome')
Expand Down
97 changes: 63 additions & 34 deletions vignettes/ecosystem.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ The scripts used to create both the mini giotto objects and mini objects are ava
```{r, eval=FALSE}
# Ensure Giotto Suite is installed
if(!"Giotto" %in% installed.packages()) {
devtools::install_github("drieslab/Giotto@suite_modular")
devtools::install_github("drieslab/Giotto")
}
library(Giotto)
Expand Down Expand Up @@ -117,9 +117,9 @@ sessionInfo()

```{r, eval=FALSE}
R version 4.3.1 (2023-06-16)
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.2
Running under: macOS Sonoma 14.2.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
Expand All @@ -128,44 +128,73 @@ LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlap
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
time zone: America/Mexico_City
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] GiottoData_0.2.6.1 Giotto_4.0.0 GiottoVisuals_0.1.0
[4] GiottoClass_0.1.0 GiottoUtils_0.1.0
[1] GiottoData_0.2.6.1 GiottoUtils_0.1.2 Giotto_4.0.2
[4] GiottoClass_0.1.2
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3
[3] lattice_0.22-5 digest_0.6.33
[5] magrittr_2.0.3 evaluate_0.23
[7] grid_4.3.1 fastmap_1.1.1
[9] jsonlite_1.8.7 Matrix_1.6-4
[11] backports_1.4.1 fansi_1.0.5
[13] scales_1.3.0 codetools_0.2-19
[15] cli_3.6.1 rlang_1.1.2
[17] XVector_0.42.0 Biobase_2.60.0
[19] munsell_0.5.0 withr_2.5.2
[21] colorRamp2_0.1.0 tools_4.3.1
[23] parallel_4.3.1 checkmate_2.3.0
[25] dplyr_1.1.4 colorspace_2.1-0
[27] ggplot2_3.4.4 BiocGenerics_0.48.1
[29] reticulate_1.34.0 png_0.1-8
[31] vctrs_0.6.5 R6_2.5.1
[33] stats4_4.3.1 lifecycle_1.0.4
[35] zlibbioc_1.48.0 S4Vectors_0.40.2
[37] IRanges_2.36.0 pkgconfig_2.0.3
[39] terra_1.7-55 pillar_1.9.0
[41] gtable_0.3.4 data.table_1.14.8
[43] glue_1.6.2 Rcpp_1.0.11
[45] xfun_0.41 tibble_3.2.1
[47] tidyselect_1.2.0 rstudioapi_0.15.0
[49] knitr_1.45 igraph_1.5.1
[51] htmltools_0.5.7 rmarkdown_2.25
[53] compiler_4.3.1
[1] colorRamp2_0.1.0 DBI_1.2.0
[3] bitops_1.0-7 biomaRt_2.58.0
[5] rlang_1.1.2 magrittr_2.0.3
[7] matrixStats_1.2.0 e1071_1.7-14
[9] compiler_4.3.2 RSQLite_2.3.4
[11] png_0.1-8 vctrs_0.6.5
[13] stringr_1.5.1 pkgconfig_2.0.3
[15] SpatialExperiment_1.12.0 crayon_1.5.2
[17] fastmap_1.1.1 backports_1.4.1
[19] dbplyr_2.4.0 magick_2.8.2
[21] XVector_0.42.0 utf8_1.2.4
[23] rmarkdown_2.25 purrr_1.0.2
[25] bit_4.0.5 xfun_0.41
[27] zlibbioc_1.48.0 cachem_1.0.8
[29] jsonlite_1.8.8 GenomeInfoDb_1.38.5
[31] progress_1.2.3 blob_1.2.4
[33] rhdf5filters_1.14.1 gmp_0.7-3
[35] DelayedArray_0.28.0 Rhdf5lib_1.24.1
[37] terra_1.7-65 parallel_4.3.2
[39] prettyunits_1.2.0 R6_2.5.1
[41] stringi_1.8.3 reticulate_1.34.0
[43] ClusterR_1.3.2 GenomicRanges_1.54.1
[45] Rcpp_1.0.11 assertthat_0.2.1
[47] SummarizedExperiment_1.32.0 knitr_1.45
[49] IRanges_2.36.0 igraph_1.6.0
[51] Matrix_1.6-4 tidyselect_1.2.0
[53] yaml_2.3.8 rstudioapi_0.15.0
[55] abind_1.4-5 codetools_0.2-19
[57] curl_5.2.0 lattice_0.21-9
[59] tibble_3.2.1 withr_2.5.2
[61] Biobase_2.62.0 KEGGREST_1.42.0
[63] evaluate_0.23 sf_1.0-15
[65] units_0.8-5 proxy_0.4-27
[67] BiocFileCache_2.10.1 xml2_1.3.6
[69] Biostrings_2.70.1 pillar_1.9.0
[71] filelock_1.0.3 MatrixGenerics_1.14.0
[73] KernSmooth_2.23-22 checkmate_2.3.1
[75] stats4_4.3.2 generics_0.1.3
[77] RCurl_1.98-1.13 S4Vectors_0.40.2
[79] hms_1.1.3 ggplot2_3.4.4
[81] munsell_0.5.0 scales_1.3.0
[83] class_7.3-22 glue_1.6.2
[85] tools_4.3.2 GiottoVisuals_0.1.1
[87] data.table_1.14.10 XML_3.99-0.16
[89] cowplot_1.1.2 rhdf5_2.46.1
[91] grid_4.3.2 AnnotationDbi_1.64.1
[93] colorspace_2.1-0 SingleCellExperiment_1.24.0
[95] GenomeInfoDbData_1.2.11 cli_3.6.2
[97] rappdirs_0.3.3 fansi_1.0.6
[99] S4Arrays_1.2.0 arrow_14.0.0.2
[101] dplyr_1.1.4 gtable_0.3.4
[103] digest_0.6.33 progressr_0.14.0
[105] BiocGenerics_0.48.1 classInt_0.4-10
[107] SparseArray_1.2.3 rjson_0.2.21
[109] memoise_2.0.1 htmltools_0.5.7
[111] lifecycle_1.0.4 httr_1.4.7
[113] bit64_4.0.5
```
111 changes: 78 additions & 33 deletions vignettes/installation.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ if(!"devtools" %in% installed.packages()) {
install.packages("devtools")
}
devtools::install_github("drieslab/Giotto@suite_modular")
devtools::install_github("drieslab/Giotto")
```


Expand Down Expand Up @@ -57,36 +57,81 @@ sessionInfo()


```{r, eval=FALSE}
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
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Mexico_City
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] Giotto_4.0.2 GiottoClass_0.1.2
loaded via a namespace (and not attached):
[1] colorRamp2_0.1.0 DBI_1.2.0
[3] bitops_1.0-7 biomaRt_2.58.0
[5] rlang_1.1.2 magrittr_2.0.3
[7] GiottoUtils_0.1.2 matrixStats_1.2.0
[9] e1071_1.7-14 compiler_4.3.2
[11] RSQLite_2.3.4 png_0.1-8
[13] vctrs_0.6.5 stringr_1.5.1
[15] pkgconfig_2.0.3 SpatialExperiment_1.12.0
[17] crayon_1.5.2 fastmap_1.1.1
[19] backports_1.4.1 dbplyr_2.4.0
[21] magick_2.8.2 XVector_0.42.0
[23] utf8_1.2.4 rmarkdown_2.25
[25] purrr_1.0.2 bit_4.0.5
[27] xfun_0.41 zlibbioc_1.48.0
[29] cachem_1.0.8 GenomeInfoDb_1.38.5
[31] progress_1.2.3 blob_1.2.4
[33] rhdf5filters_1.14.1 gmp_0.7-3
[35] DelayedArray_0.28.0 Rhdf5lib_1.24.1
[37] terra_1.7-65 parallel_4.3.2
[39] prettyunits_1.2.0 R6_2.5.1
[41] stringi_1.8.3 ClusterR_1.3.2
[43] GenomicRanges_1.54.1 Rcpp_1.0.11
[45] assertthat_0.2.1 SummarizedExperiment_1.32.0
[47] knitr_1.45 IRanges_2.36.0
[49] Matrix_1.6-4 tidyselect_1.2.0
[51] yaml_2.3.8 rstudioapi_0.15.0
[53] abind_1.4-5 codetools_0.2-19
[55] curl_5.2.0 lattice_0.21-9
[57] tibble_3.2.1 Biobase_2.62.0
[59] KEGGREST_1.42.0 evaluate_0.23
[61] sf_1.0-15 units_0.8-5
[63] proxy_0.4-27 BiocFileCache_2.10.1
[65] xml2_1.3.6 Biostrings_2.70.1
[67] pillar_1.9.0 filelock_1.0.3
[69] MatrixGenerics_1.14.0 KernSmooth_2.23-22
[71] checkmate_2.3.1 stats4_4.3.2
[73] generics_0.1.3 RCurl_1.98-1.13
[75] S4Vectors_0.40.2 hms_1.1.3
[77] ggplot2_3.4.4 munsell_0.5.0
[79] scales_1.3.0 class_7.3-22
[81] glue_1.6.2 tools_4.3.2
[83] GiottoVisuals_0.1.1 data.table_1.14.10
[85] XML_3.99-0.16 cowplot_1.1.2
[87] rhdf5_2.46.1 grid_4.3.2
[89] AnnotationDbi_1.64.1 colorspace_2.1-0
[91] SingleCellExperiment_1.24.0 GenomeInfoDbData_1.2.11
[93] cli_3.6.2 rappdirs_0.3.3
[95] fansi_1.0.6 S4Arrays_1.2.0
[97] arrow_14.0.0.2 dplyr_1.1.4
[99] gtable_0.3.4 digest_0.6.33
[101] progressr_0.14.0 BiocGenerics_0.48.1
[103] classInt_0.4-10 SparseArray_1.2.3
[105] rjson_0.2.21 memoise_2.0.1
[107] htmltools_0.5.7 lifecycle_1.0.4
[109] httr_1.4.7 bit64_4.0.5
```
119 changes: 88 additions & 31 deletions vignettes/structure.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -640,35 +640,92 @@ sessionInfo()
```

```{r, eval=FALSE}
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.8 GiottoData_0.2.2 Giotto_3.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 pillar_1.9.0 compiler_4.2.1 tools_4.2.1
[5] digest_0.6.31 jsonlite_1.8.4 evaluate_0.21 lifecycle_1.0.3
[9] tibble_3.2.1 gtable_0.3.3 lattice_0.20-45 png_0.1-8
[13] pkgconfig_2.0.3 rlang_1.1.1 igraph_1.4.2 Matrix_1.5-4
[17] cli_3.6.1 rstudioapi_0.14 parallel_4.2.1 yaml_2.3.7
[21] xfun_0.39 fastmap_1.1.1 terra_1.7-39 withr_2.5.0
[25] dplyr_1.1.2 knitr_1.42 generics_0.1.3 vctrs_0.6.2
[29] rprojroot_2.0.3 grid_4.2.1 tidyselect_1.2.0 here_1.0.1
[33] reticulate_1.28 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[37] rmarkdown_2.21 ggplot2_3.4.2 magrittr_2.0.3 scales_1.2.1
[41] codetools_0.2-18 htmltools_0.5.5 colorspace_2.1-0 utf8_1.2.3
[45] munsell_0.5.0
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Mexico_City
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] data.table_1.14.10 GiottoData_0.2.6.1 GiottoUtils_0.1.2
[4] Giotto_4.0.2 GiottoClass_0.1.2
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 jsonlite_1.8.8
[3] magrittr_2.0.3 magick_2.8.2
[5] rmarkdown_2.25 fs_1.6.3
[7] zlibbioc_1.48.0 vctrs_0.6.5
[9] memoise_2.0.1 RCurl_1.98-1.13
[11] terra_1.7-65 usethis_2.2.2
[13] htmltools_0.5.7 S4Arrays_1.2.0
[15] progress_1.2.3 curl_5.2.0
[17] Rhdf5lib_1.24.1 SparseArray_1.2.3
[19] rhdf5_2.46.1 KernSmooth_2.23-22
[21] htmlwidgets_1.6.4 cachem_1.0.8
[23] igraph_1.6.0 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3
[27] Matrix_1.6-4 R6_2.5.1
[29] fastmap_1.1.1 GenomeInfoDbData_1.2.11
[31] MatrixGenerics_1.14.0 shiny_1.8.0
[33] digest_0.6.33 colorspace_2.1-0
[35] AnnotationDbi_1.64.1 S4Vectors_0.40.2
[37] pkgload_1.3.3 GenomicRanges_1.54.1
[39] RSQLite_2.3.4 filelock_1.0.3
[41] progressr_0.14.0 fansi_1.0.6
[43] httr_1.4.7 abind_1.4-5
[45] compiler_4.3.2 proxy_0.4-27
[47] remotes_2.4.2.1 bit64_4.0.5
[49] withr_2.5.2 backports_1.4.1
[51] DBI_1.2.0 pkgbuild_1.4.3
[53] biomaRt_2.58.0 sessioninfo_1.2.2
[55] rappdirs_0.3.3 DelayedArray_0.28.0
[57] rjson_0.2.21 classInt_0.4-10
[59] GiottoVisuals_0.1.1 tools_4.3.2
[61] units_0.8-5 httpuv_1.6.13
[63] glue_1.6.2 rhdf5filters_1.14.1
[65] promises_1.2.1 grid_4.3.2
[67] sf_1.0-15 checkmate_2.3.1
[69] generics_0.1.3 gtable_0.3.4
[71] class_7.3-22 hms_1.1.3
[73] xml2_1.3.6 utf8_1.2.4
[75] XVector_0.42.0 BiocGenerics_0.48.1
[77] pillar_1.9.0 stringr_1.5.1
[79] later_1.3.2 dplyr_1.1.4
[81] BiocFileCache_2.10.1 lattice_0.21-9
[83] gmp_0.7-3 bit_4.0.5
[85] tidyselect_1.2.0 SingleCellExperiment_1.24.0
[87] Biostrings_2.70.1 miniUI_0.1.1.1
[89] knitr_1.45 IRanges_2.36.0
[91] SummarizedExperiment_1.32.0 stats4_4.3.2
[93] xfun_0.41 Biobase_2.62.0
[95] devtools_2.4.5 matrixStats_1.2.0
[97] stringi_1.8.3 yaml_2.3.8
[99] evaluate_0.23 codetools_0.2-19
[101] tibble_3.2.1 colorRamp2_0.1.0
[103] cli_3.6.2 arrow_14.0.0.2
[105] xtable_1.8-4 reticulate_1.34.0
[107] munsell_0.5.0 Rcpp_1.0.11
[109] GenomeInfoDb_1.38.5 dbplyr_2.4.0
[111] png_0.1-8 XML_3.99-0.16
[113] parallel_4.3.2 ellipsis_0.3.2
[115] ggplot2_3.4.4 assertthat_0.2.1
[117] blob_1.2.4 prettyunits_1.2.0
[119] ClusterR_1.3.2 profvis_0.3.8
[121] urlchecker_1.0.1 bitops_1.0-7
[123] SpatialExperiment_1.12.0 scales_1.3.0
[125] e1071_1.7-14 purrr_1.0.2
[127] crayon_1.5.2 rlang_1.1.2
[129] cowplot_1.1.2 KEGGREST_1.42.0
```

0 comments on commit e6a48c6

Please sign in to comment.