Cluster tree module

Usage

clustreeUI(id, panel)

clustreeServer(id, obj, filtered, args, reload_global, config)

Arguments

id: Input id
panel: string, can be 'sidebar' or 'main'
obj: Cascade app object
filtered: cell barcodes for filtering object
args: reactive list with global args, 'grp_by' for grouping variable and 'dimred' for which dimension reduction to use
reload_global: reactive to reload module
config: reactive list with config settings

Value

UI returns sidebar/main panel UI elements for the cluster tree Server called for the side effect of rendering cluster tree plots.

Examples

if (FALSE) { # interactive()
# example obj
obj <- make_example_seurat_object()

# prep metadata
metadata <- obj[[]]
metadata_levels <- lapply(
  metadata[c("cluster", "condition", "orig.ident", "seurat_clusters")],
  levels
)

# get grouping vars and colors
grouping_vars <- names(metadata_levels)
names(grouping_vars) <- paste0(
  grouping_vars,
  " (n = ",
  lengths(metadata_levels),
  ")"
)
cluster_colors <- lapply(metadata_levels, function(lvls) {
  stats::setNames(rep_len(c("#4477aa", "#cc6677"), length(lvls)), lvls)
})

app_object <- list(
  rds = obj,
  obj_type = "seurat",
  metadata = metadata,
  metadata_levels = list(
    all = metadata_levels,
    filtered = metadata_levels
  ),
  cluster_colors = cluster_colors,
  grouping_vars = grouping_vars,
  spatial_coords = NULL,
  imagerow_max = NULL,
  imagerow_min = NULL
)

global_args <- list(
  grp_by = "cluster",
  dimred = "umap"
)

config <- get_config()

ui <- shiny::fluidPage(
  shinyjs::useShinyjs(),
  shiny::sidebarLayout(
    shiny::sidebarPanel(clustreeUI("clustree", "sidebar")),
    shiny::mainPanel(clustreeUI("clustree", "main"))
  )
)

server <- function(input, output, session) {
  clustreeServer(
    "clustree",
    obj = app_object,
    filtered = shiny::reactive({ colnames(obj) }),
    args = shiny::reactive({ global_args }),
    reload_global = shiny::reactiveVal(0),
    config = shiny::reactive({ config })
  )
}

shiny::shinyApp(ui, server)
}