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Merge pull request #910 from josschavezf/suite
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update website examples
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@josschavezf
josschavezf authored Feb 13, 2024
2 parents a81d841 + 13ce19a commit 11f41ea
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188 changes: 117 additions & 71 deletions vignettes/codex_mouse_spleen.Rmd
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60 changes: 37 additions & 23 deletions vignettes/configuration.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ if(retry_install){
if(.Platform[['OS.type']] == 'unix') {
conda_full_path = paste0(partial_conda_path,'/','bin/conda')
conda_full_path = paste0(partial_path_to_conda,'/','bin/conda')
# Remove all previous installations
reticulate::conda_remove(envname = env_location,
Expand All @@ -233,7 +233,7 @@ if(retry_install){
python_version = python_version)
}
else if(.Platform[['OS.type']] == 'windows'){
conda_full_path = paste0(partial_conda_path,'/','condabin/conda.bat')
conda_full_path = paste0(partial_path_to_conda,'/','condabin/conda.bat')
# Remove all previous installations
reticulate::conda_remove(envname = env_location,
Expand Down Expand Up @@ -276,36 +276,50 @@ 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)
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1
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-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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
[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
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GiottoData_0.1.0 Giotto_3.2.1
[1] Giotto_4.0.2 GiottoClass_0.1.3
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 png_0.1-7
[13] pkgconfig_2.0.3 rlang_1.1.0 Matrix_1.5-1 cli_3.4.1
[17] rstudioapi_0.14 parallel_4.2.2 yaml_2.3.7 xfun_0.38
[21] fastmap_1.1.0 terra_1.7-18 dplyr_1.1.1 knitr_1.42
[25] rappdirs_0.3.3 generics_0.1.3 vctrs_0.6.1 grid_4.2.2
[29] tidyselect_1.2.0 reticulate_1.26 glue_1.6.2 data.table_1.14.6
[33] R6_2.5.1 fansi_1.0.4 rmarkdown_2.21 ggplot2_3.4.1
[37] magrittr_2.0.3 scales_1.2.1 codetools_0.2-18 htmltools_0.5.4
[41] colorspace_2.1-0 utf8_1.2.3 munsell_0.5.0
[1] SummarizedExperiment_1.32.0 gtable_0.3.4 rjson_0.2.21
[4] xfun_0.42 ggplot2_3.4.4 Biobase_2.62.0
[7] lattice_0.22-5 vctrs_0.6.5 tools_4.3.2
[10] bitops_1.0-7 generics_0.1.3 parallel_4.3.2
[13] stats4_4.3.2 tibble_3.2.1 fansi_1.0.6
[16] colorRamp2_0.1.0 pkgconfig_2.0.3 Matrix_1.6-5
[19] checkmate_2.3.1 data.table_1.15.0 S4Vectors_0.40.2
[22] lifecycle_1.0.4 GenomeInfoDbData_1.2.11 compiler_4.3.2
[25] GiottoUtils_0.1.5 munsell_0.5.0 terra_1.7-71
[28] codetools_0.2-19 GenomeInfoDb_1.38.6 htmltools_0.5.7
[31] RCurl_1.98-1.14 yaml_2.3.8 pillar_1.9.0
[34] crayon_1.5.2 SingleCellExperiment_1.24.0 DelayedArray_0.28.0
[37] magick_2.8.2 abind_1.4-5 gtools_3.9.5
[40] tidyselect_1.2.0 digest_0.6.34 dplyr_1.1.4
[43] rprojroot_2.0.4 fastmap_1.1.1 grid_4.3.2
[46] here_1.0.1 colorspace_2.1-0 cli_3.6.2
[49] SparseArray_1.2.3 magrittr_2.0.3 S4Arrays_1.2.0
[52] utf8_1.2.4 withr_3.0.0 backports_1.4.1
[55] scales_1.3.0 rmarkdown_2.25 XVector_0.42.0
[58] matrixStats_1.2.0 reticulate_1.35.0 GiottoVisuals_0.1.4
[61] png_0.1-8 SpatialExperiment_1.12.0 evaluate_0.23
[64] knitr_1.45 GenomicRanges_1.54.1 IRanges_2.36.0
[67] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
[70] BiocGenerics_0.48.1 rstudioapi_0.15.0 jsonlite_1.8.8
[73] R6_2.5.1 MatrixGenerics_1.14.0 zlibbioc_1.48.0
```
188 changes: 138 additions & 50 deletions vignettes/github_issues.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ R.version.string
```

```{r, eval=FALSE}
R version 4.0.4 (2021-02-15)
R version 4.3.2 (2023-10-31)
```

- What version of Giotto are you using?
Expand All @@ -32,30 +32,74 @@ packageVersion("Giotto")
```

```{r, eval=FALSE}
2.0.0.9044
4.0.2
```

- Are you using the Giotto environment or your own python path?

```{r, eval=FALSE}
# Check Giotto environment
Giotto:::checkGiottoEnvironment()
Giotto::checkGiottoEnvironment()
```

```{r, eval=FALSE}
giotto environment found at
/Users/natalie_dr/Library/r-miniconda/envs/giotto_env/bin/pythonw
/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw
```

- Show sequential processing steps/commands in the Giotto object

```{r, eval=FALSE}
Giotto:::showProcessingSteps(my_giotto_object)
Giotto::showProcessingSteps(my_giotto_object)
```

```{r, eval=FALSE}
Processing steps:
0_normalize
1_subset
2_filter
name info: tag tag
3_feat_stats
4_cell_stats
5_hvf
name info: hvf HVFplot
6_pca
7_umap
8_tsne
9_nn_network
10_cluster
name info: leiden_clus sNN.pca
11_delaunay_spatial_network
name info: Delaunay_network
12_spatial_network
name info: spatial_network
13_create_metafeat
name info: cluster_metagene
14_pca
name info: custom_pca
15_umap
name info: custom_pca custom_umap
16_nn_network
name info: custom_pca custom_NN
17_cluster
name info: custom_leiden custom_NN
```

- Show the structure of the Giotto object
Expand All @@ -65,48 +109,90 @@ str(my_giotto_object, max.level = 3)
```

```{r, eval=FALSE}
Formal class 'giotto' [package "Giotto"] with 20 slots
..@ expression :List of 1
.. ..$ rna:List of 3
..@ expression_feat : chr "rna"
..@ spatial_locs :List of 1
.. ..$ raw:Classes ‘data.table’ and 'data.frame': 73655 obs. of 4 variables:
.. .. ..- attr(*, ".internal.selfref")=<externalptr>
..@ spatial_info : NULL
..@ cell_metadata :List of 1
.. ..$ rna:Classes ‘data.table’ and 'data.frame': 73655 obs. of 1 variable:
.. .. ..- attr(*, ".internal.selfref")=<externalptr>
..@ feat_metadata :List of 1
.. ..$ rna:Classes ‘data.table’ and 'data.frame': 161 obs. of 1 variable:
.. .. ..- attr(*, ".internal.selfref")=<externalptr>
..@ feat_info : NULL
..@ cell_ID : chr [1:73655] "cell_1" "cell_2" "cell_3" "cell_4" ...
..@ feat_ID :List of 1
.. ..$ rna: chr [1:161] "Ace2" "Adora2a" "Aldh1l1" "Amigo2" ...
..@ spatial_network : NULL
..@ spatial_grid : NULL
..@ spatial_enrichment : NULL
..@ dimension_reduction: NULL
..@ nn_network : NULL
..@ images : NULL
..@ parameters :List of 1
.. ..$ 0_normalize: Named chr [1:13] "my_giotto_object" "standard" "TRUE" "6000" ...
.. .. ..- attr(*, "names")= chr [1:13] "gobject" "norm_methods" "library_size_norm" "scalefactor" ...
..@ instructions :List of 11
.. ..$ python_path: chr "/Users/natalie_dr/Library/r-miniconda/envs/giotto_env/bin/pythonw"
.. ..$ show_plot : logi TRUE
.. ..$ return_plot: logi TRUE
.. ..$ save_plot : logi FALSE
.. ..$ save_dir : chr "/Users/natalie_dr/Desktop/my_giotto/giotto_user_help"
.. ..$ plot_format: chr "png"
.. ..$ dpi : num 300
.. ..$ units : chr "in"
.. ..$ height : num 9
.. ..$ width : num 9
.. ..$ is_docker : logi FALSE
..@ offset_file : NULL
..@ OS_platform : chr "unix"
..@ join_info : NULL
Formal class 'giotto' [package "Giotto"] with 23 slots
..@ expression :List of 1
.. ..$ cell:List of 1
..@ expression_feat : chr "rna"
..@ spatial_locs :List of 1
.. ..$ cell:List of 1
..@ spatial_info : NULL
..@ cell_metadata :List of 1
.. ..$ cell:List of 1
..@ feat_metadata :List of 1
.. ..$ cell:List of 1
..@ feat_info : NULL
..@ cell_ID :List of 1
.. ..$ cell: chr [1:624] "AAAGGGATGTAGCAAG-1" "AAATGGCATGTCTTGT-1" "AAATGGTCAATGTGCC-1" "AAATTAACGGGTAGCT-1" ...
..@ feat_ID :List of 1
.. ..$ rna: chr [1:634] "Gna12" "Ccnd2" "Btbd17" "Sox9" ...
..@ spatial_network :List of 1
.. ..$ cell:List of 2
..@ spatial_grid : NULL
..@ spatial_enrichment :List of 1
.. ..$ cell:List of 1
..@ dimension_reduction:List of 1
.. ..$ cells:List of 1
..@ nn_network :List of 1
.. ..$ cell:List of 1
..@ images : NULL
..@ largeImages :List of 1
.. ..$ image:Formal class 'giottoLargeImage' [package "Giotto"] with 13 slots
..@ parameters :List of 18
.. ..$ 0_normalize : Named chr [1:14] "mini_visium" "raw" "standard" "TRUE" ...
.. .. ..- attr(*, "names")= chr [1:14] "gobject" "expression_values" "norm_methods" "library_size_norm" ...
.. ..$ 1_subset : Named chr [1:12] "gobject" "spat_unit" "feat_type" "selected_cell_ids" ...
.. .. ..- attr(*, "names")= chr [1:12] "gobject" "spat_unit" "feat_type" "cell_ids" ...
.. ..$ 2_filter : Named chr [1:13] "mini_visium" "raw" "1" "5" ...
.. .. ..- attr(*, "names")= chr [1:13] "gobject" "expression_values" "expression_threshold" "feat_det_in_min_cells" ...
.. ..$ 3_feat_stats : Named chr [1:4] "mini_visium" "normalized" "0" "TRUE"
.. .. ..- attr(*, "names")= chr [1:4] "gobject" "expression_values" "detection_threshold" "return_gobject"
.. ..$ 4_cell_stats : Named chr [1:4] "mini_visium" "normalized" "0" "TRUE"
.. .. ..- attr(*, "names")= chr [1:4] "gobject" "expression_values" "detection_threshold" "return_gobject"
.. ..$ 5_hvf : Named chr [1:17] "mini_visium" "normalized" "cov_groups" "FALSE" ...
.. .. ..- attr(*, "names")= chr [1:17] "gobject" "expression_values" "method" "reverse_log_scale" ...
.. ..$ 6_pca : Named chr [1:15] "mini_visium" "normalized" "cells" "hvf" ...
.. .. ..- attr(*, "names")= chr [1:15] "gobject" "expression_values" "reduction" "feats_to_use" ...
.. ..$ 7_umap : Named chr [1:17] "mini_visium" "normalized" "cells" "pca" ...
.. .. ..- attr(*, "names")= chr [1:17] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
.. ..$ 8_tsne : Named chr [1:14] "mini_visium" "normalized" "cells" "pca" ...
.. .. ..- attr(*, "names")= chr [1:14] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
.. ..$ 9_nn_network : Named chr [1:11] "mini_visium" "sNN" "pca" "1:5" ...
.. .. ..- attr(*, "names")= chr [1:11] "gobject" "type" "dim_reduction_to_use" "dimensions_to_use" ...
.. ..$ 10_cluster : Named chr [1:11] "mini_visium" "leiden_clus" "sNN" "sNN.pca" ...
.. .. ..- attr(*, "names")= chr [1:11] "gobject" "name" "nn_network_to_use" "network_name" ...
.. ..$ 11_delaunay_spatial_network: Named chr [1:4] "dimensions: sdimx and sdimy" "deldir" "auto" "Delaunay_network"
.. .. ..- attr(*, "names")= chr [1:4] "dimensions used" "method" "maximum distance threshold" "name of spatial network"
.. ..$ 12_spatial_network : Named chr [1:4] "10" "all" "400" "spatial_network"
.. .. ..- attr(*, "names")= chr [1:4] "k neighbours" "dimensions used" "maximum distance threshold" "name of spatial network"
.. ..$ 13_create_metafeat : Named chr [1:5] "mini_visium" "normalized" "cluster_genes" "cluster_metagene" ...
.. .. ..- attr(*, "names")= chr [1:5] "gobject" "expression_values" "feat_clusters" "name" ...
.. ..$ 14_pca : Named chr [1:16] "mini_visium" "normalized" "cells" "custom_pca" ...
.. .. ..- attr(*, "names")= chr [1:16] "gobject" "expression_values" "reduction" "name" ...
.. ..$ 15_umap : Named chr [1:19] "mini_visium" "normalized" "cells" "pca" ...
.. .. ..- attr(*, "names")= chr [1:19] "gobject" "expression_values" "reduction" "dim_reduction_to_use" ...
.. ..$ 16_nn_network : Named chr [1:13] "mini_visium" "sNN" "pca" "custom_pca" ...
.. .. ..- attr(*, "names")= chr [1:13] "gobject" "type" "dim_reduction_to_use" "dim_reduction_name" ...
.. ..$ 17_cluster : Named chr [1:11] "mini_visium" "custom_leiden" "sNN" "custom_NN" ...
.. .. ..- attr(*, "names")= chr [1:11] "gobject" "name" "nn_network_to_use" "network_name" ...
..@ instructions :List of 13
.. ..$ python_path : chr "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
.. ..$ show_plot : logi TRUE
.. ..$ return_plot : logi FALSE
.. ..$ save_plot : logi FALSE
.. ..$ save_dir : logi NA
.. ..$ plot_format : chr "png"
.. ..$ dpi : num 300
.. ..$ units : chr "in"
.. ..$ height : num 9
.. ..$ width : num 9
.. ..$ is_docker : logi FALSE
.. ..$ active_spat_unit: chr "cell"
.. ..$ active_feat_type: chr "rna"
..@ offset_file : NULL
..@ OS_platform : chr "unix"
..@ join_info : NULL
..@ multiomics : NULL
..@ h5_file : NULL
```

### Warning Messages
Expand All @@ -115,7 +201,7 @@ Formal class 'giotto' [package "Giotto"] with 20 slots

```{r, eval=FALSE}
my_giotto_object <- createGiottoObject(raw_exprs = "path/to/expression/data",
spatial_locs = "path/to/spatial/data")
spatial_locs = "path/to/spatial/data")
```

```{r, eval=FALSE}
Expand All @@ -128,7 +214,7 @@ In createGiottoObject(raw_exprs = "/Users/username/path/to/data", :

```{r, eval=FALSE}
my_giotto_object <- createGiottoObject(expression = "path/to/expression/data",
spatial_locs = "path/to/spatial/data")
spatial_locs = "path/to/spatial/data")
```

### Errors
Expand Down Expand Up @@ -191,6 +277,8 @@ I am having trouble adjusting my Giotto matix. I have inputted the
following code:

```{r, eval=FALSE}
my_giotto_object <- GiottoData::loadGiottoMini("visium")
my_giotto_object <- adjustGiottoMatrix(gobject = my_giotto_object,
expression_values = c('normalized'),
covariate_columns = c('nr_genes',
Expand All @@ -203,7 +291,7 @@ I expected that my matrix would be appropriately adjusted, but I got the followi
Error in adjustGiottoMatrix(gobject = my_giotto_object, expression_values = c("normalized"): covariate column name(s) were not found in the cell metadata
```

For more context, I am running R version 4.04 and Giotto version 2.0.0.9044. I can send you the data I used if necessary.
For more context, I am running R version 4.3.2 and Giotto version 4.0.2. I can send you the data I used if necessary.

### Example of a Bad GitHub issue

Expand Down
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