Skip to content

update vignette #130

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
josschavezf merged 2 commits into from
May 21, 2026
Merged

update vignette #130

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e3e382b
update vignette
josschavezf May 21, 2026
c3e3ad2
Merge branch 'website' of https://github.com/josschavezf/GiottoVisual…
josschavezf May 21, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
67 changes: 62 additions & 5 deletions vignettes/intro_to_GiottoVisuals.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
---
title: "Introduction to GiottoVisuals"
output: rmarkdown::html_vignette
output:
html_document:
number_sections: true
toc: true
pkgdown:
as_is: true
vignette: >
%\VignetteIndexEntry{Introduction to GiottoVisuals}
%\VignetteEngine{knitr::rmarkdown}
Expand Down Expand Up @@ -52,13 +57,13 @@ Package:

Load the package

```{r}
```{r, eval=FALSE}
library(GiottoVisuals)
```

Create a small Giotto object

```{r}
```{r, eval=FALSE}
expression_matrix <- matrix(rnorm(1000), nrow = 10)
colnames(expression_matrix) <- paste0("cell_", 1:100)
rownames(expression_matrix) <- paste0("gene_", 1:10)
Expand All @@ -77,14 +82,66 @@ giotto_object <- GiottoClass::createGiottoObject(

Plot the spatial locations

```{r}
```{r, eval=FALSE}
spatPlot2D(giotto_object)
```


## Session Info

```{r}
```{r, eval=FALSE}
sessionInfo()
```


```{r, eval=FALSE}
R version 4.5.3 (2026-03-11)
Platform: x86_64-apple-darwin20
Running under: macOS Tahoe 26.4.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

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
tzcode source: internal

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

other attached packages:
[1] GiottoVisuals_0.2.15

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.40.0 gtable_0.3.6 rjson_0.2.23
[4] xfun_0.57 ggplot2_4.0.2 htmlwidgets_1.6.4
[7] ggrepel_0.9.8 Biobase_2.70.0 lattice_0.22-9
[10] vctrs_0.7.3 tools_4.5.3 generics_0.1.4
[13] parallel_4.5.3 stats4_4.5.3 tibble_3.3.1
[16] colorRamp2_0.1.0 pkgconfig_2.0.3 Matrix_1.7-4
[19] data.table_1.18.2.1 checkmate_2.3.4 RColorBrewer_1.1-3
[22] S7_0.2.1 S4Vectors_0.48.0 lifecycle_1.0.5
[25] compiler_4.5.3 farver_2.1.2 GiottoUtils_0.2.5
[28] terra_1.9-11 Seqinfo_1.0.0 codetools_0.2-20
[31] scattermore_1.2 htmltools_0.5.9 GiottoClass_0.5.1
[34] yaml_2.3.12 lazyeval_0.2.2 plotly_4.12.0
[37] tidyr_1.3.2 pillar_1.11.1 SingleCellExperiment_1.32.0
[40] DelayedArray_0.36.1 magick_2.9.1 abind_1.4-8
[43] gtools_3.9.5 tidyselect_1.2.1 digest_0.6.39
[46] purrr_1.2.2 dplyr_1.2.1 labeling_0.4.3
[49] cowplot_1.2.0 fastmap_1.2.0 grid_4.5.3
[52] colorspace_2.1-2 cli_3.6.6 SparseArray_1.10.10
[55] magrittr_2.0.5 S4Arrays_1.10.1 withr_3.0.2
[58] scales_1.4.0 backports_1.5.1 rmarkdown_2.31
[61] XVector_0.50.0 httr_1.4.8 matrixStats_1.5.0
[64] igraph_2.2.2 otel_0.2.0 reticulate_1.45.0
[67] png_0.1-9 SpatialExperiment_1.20.0 evaluate_1.0.5
[70] knitr_1.51 GenomicRanges_1.62.1 IRanges_2.44.0
[73] viridisLite_0.4.3 rlang_1.2.0 Rcpp_1.1.1
[76] glue_1.8.1 BiocGenerics_0.56.0 rstudioapi_0.18.0
[79] jsonlite_2.0.0 R6_2.6.1 MatrixGenerics_1.22.0
```

Loading