This function runs the shiny application that allows users to interact with the Visium spatial transcriptomics data from LIBD (by default) or any other data that you have shaped according to our object structure.

run_app(
spe = fetch_data(type = "spe"),
sce_layer = fetch_data(type = "sce_layer"),
modeling_results = fetch_data(type = "modeling_results"),
sig_genes = sig_genes_extract_all(n = nrow(sce_layer), modeling_results =
modeling_results, sce_layer = sce_layer),
docs_path = system.file("app", "www", package = "spatialLIBD"),
title = "spatialLIBD",
spe_discrete_vars = c("spatialLIBD", "GraphBased", "ManualAnnotation", "Maynard",
"Martinowich", paste0("SNN_k50_k", 4:28), "SpatialDE_PCA", "SpatialDE_pool_PCA",
"HVG_PCA", "pseudobulk_PCA", "markers_PCA", "SpatialDE_UMAP", "SpatialDE_pool_UMAP",
"HVG_UMAP", "pseudobulk_UMAP", "markers_UMAP", "SpatialDE_PCA_spatial",
"SpatialDE_pool_PCA_spatial", "HVG_PCA_spatial", "pseudobulk_PCA_spatial",
"markers_PCA_spatial", "SpatialDE_UMAP_spatial", "SpatialDE_pool_UMAP_spatial",
"HVG_UMAP_spatial", "pseudobulk_UMAP_spatial",
"markers_UMAP_spatial"),
spe_continuous_vars = c("cell_count", "sum_umi", "sum_gene", "expr_chrM",
"expr_chrM_ratio"),
default_cluster = "spatialLIBD",
...
)

## Arguments

spe

Defaults to the output of fetch_data(type = 'spe'). This is a SpatialExperiment-class object with the spot-level Visium data and information required for visualizing the histology. See fetch_data() for more details.

sce_layer

Defaults to the output of fetch_data(type = 'sce_layer'). This is a SingleCellExperiment object with the spot-level Visium data compressed via pseudo-bulking to the layer-level (group-level) resolution. See fetch_data() for more details.

modeling_results

Defaults to the output of fetch_data(type = 'modeling_results'). This is a list of tables with the columns f_stat_* or t_stat_* as well as p_value_* and fdr_* plus ensembl. The column name is used to extract the statistic results, the p-values, and the FDR adjusted p-values. Then the ensembl column is used for matching in some cases. See fetch_data() for more details.

sig_genes

The output of sig_genes_extract_all() which is a table in long format with the modeling results. You can subset this if the object requires too much memory.

docs_path

A character(1) specifying the path to the directory containing the website documentation files. The directory has to contain the files: documentation_sce_layer.md, documentation_spe.md, favicon.ico, footer.html and README.md.

title

A character(1) specifying the title for the app.

spe_discrete_vars

A character() vector of discrete variables that will be available to visualize in the app. Basically, the set of variables with spot-level groups. They will have to be present in colData(spe).

spe_continuous_vars

A character() vector of continuous variables that will be available to visualize in the app using the same scale as genes. They will have to be present in colData(sce).

default_cluster

A character(1) with the name of the main cluster (discrete) variable to use. It will have to be present in both colData(spe) and colData(sce_layer).

...

Other arguments passed to the list of golem options for running the application.

## Value

A shiny.appobj that contains the input data.

## Details

If you don't have the pseudo-bulked analysis results like we computed them in our project https://doi.org/10.1038/s41593-020-00787-0 you can set sce_layer, modeling_results and sig_genes to NULL. Doing so will disable the pseudo-bulked portion of the web application. See the examples for one such case as well as the vignette that describes how you can use spatialLIBD with public data sets provided by 10x Genomics. That vignette is available at http://research.libd.org/spatialLIBD/articles/TenX_data_download.html.

## Examples

if (FALSE) {
## using fetch_data(). If this is the first time you have run this,
## the files will need to be cached by ExperimentHub. Otherwise it
if (enough_ram(4e9)) {
## Obtain the necessary data
if (!exists("spe")) spe <- fetch_data("spe")

## Create the interactive website
run_app(spe)

## You can also run a custom version without the pseudo-bulked
## layer information. This is useful if you are only interested
## in the spatial transcriptomics features.
run_app(spe,
sce_layer = NULL, modeling_results = NULL, sig_genes = NULL,
title = "spatialLIBD without layer info"
)

## When using shinyapps.io aim for less than 3 GB of RAM with your
## objects. Check each input object with:
## lobstr::obj_size(x)
## Do not create the large input objects on the app.R script before
## subsetting them. Do this outside app.R since the app.R script is
## run at shinyapps.io, so subsetting on that script to reduce the
## memory load is pointless. You have to do it outside of app.R.
}

## How to run locally the spatialDLPFC Sp09 spatialLIBD app. That is,
## from http://research.libd.org/spatialDLPFC/#interactive-websites
## how to run https://libd.shinyapps.io/spatialDLPFC_Visium_Sp09 locally.
if (enough_ram(9e9)) {
spe <- fetch_data("spatialDLPFC_Visium")
sce_pseudo <- fetch_data("spatialDLPFC_Visium_pseudobulk")
modeling_results <- fetch_data("spatialDLPFC_Visium_modeling_results")

## These are optional commands to further reduce the memory required.
#
## Keep only the "lowres" images. Reduces the object from 6.97 GB to 4.59 GB
# imgData(spe) <- imgData(spe)[imgData(spe)$image_id == "lowres", ] ## Drop the regular counts (keep only the logcounts). Reduces the object ## from 4.59 GB to 2.45 GB. # counts(spe) <- NULL ## For sig_genes_extract_all() to work sce_pseudo$spatialLIBD <- sce_pseudo$BayesSpace ## Compute the significant genes sig_genes <- sig_genes_extract_all( n = nrow(sce_pseudo), modeling_results = modeling_results, sce_layer = sce_pseudo ) ## Reduce the memory from 423.73 MB to 78.88 MB lobstr::obj_size(sig_genes) sig_genes$in_rows <- NULL
sig_genes$in_rows_top20 <- NULL lobstr::obj_size(sig_genes) ## Specify the default variable spe$BayesSpace <- spe$BayesSpace_harmony_09 ## Get all variables vars <- colnames(colData(spe)) ## Set default cluster colors colors_BayesSpace <- Polychrome::palette36.colors(28) names(colors_BayesSpace) <- c(1:28) m <- match(as.character(spe$BayesSpace_harmony_09), names(colors_BayesSpace))
stopifnot(all(!is.na(m)))
spe$BayesSpace_colors <- spe$BayesSpace_harmony_09_colors <- colors_BayesSpace[m]

temp_www <- file.path(tempdir(), "www")
dir.create(temp_www)
)
"https://raw.githubusercontent.com/LieberInstitute/spatialDLPFC/main/code/deploy_app_k09/www/documentation_sce_layer.md",
file.path(temp_www, "documentation_sce_layer.md")
)
"https://raw.githubusercontent.com/LieberInstitute/spatialDLPFC/main/code/deploy_app_k09/www/documentation_spe.md",
file.path(temp_www, "documentation_spe.md")
)
"https://raw.githubusercontent.com/LieberInstitute/spatialDLPFC/main/img/favicon.ico",
file.path(temp_www, "favicon.ico")
)
"https://raw.githubusercontent.com/LieberInstitute/spatialDLPFC/main/code/deploy_app_k09/www/footer.html",
file.path(temp_www, "footer.html")
)
list.files(temp_www)

## Run the app locally
run_app(
spe,
sce_layer = sce_pseudo,
modeling_results = modeling_results,
sig_genes = sig_genes,
title = "spatialDLPFC, Visium, Sp09",
spe_discrete_vars = c( # this is the variables for the spe object not the sce_pseudo object
"BayesSpace",
"ManualAnnotation",
vars[grep("^SpaceRanger_|^scran_", vars)],
vars[grep("^BayesSpace_harmony", vars)],
vars[grep("^BayesSpace_pca", vars)],
"graph_based_PCA_within",
"PCA_SNN_k10_k7",
"Harmony_SNN_k10_k7",
"manual_layer_label",
"wrinkle_type",
"BayesSpace_colors"
),
spe_continuous_vars = c(
"sum_umi",
"sum_gene",
"expr_chrM",
"expr_chrM_ratio",
vars[grep("^VistoSeg_", vars)],
vars[grep("^layer_", vars)],