Create 10x VisiumHD Giotto Object from Segmented Outputs

Convenience function to create a Giotto object from a VisiumHD `segmented_outputs` folder (Space Ranger v4+). Point `segmented_outputs_dir` directly at the `segmented_outputs` directory. For lower-level loading of individual pieces of data, see [importVisiumHD()].

Transcript loading (2 µm bin data) requires access to the `binned_outputs` directory. When `load_transcripts = TRUE` the function first tries to auto-detect `binned_outputs` as a sibling directory next to `segmented_outputs`. If it cannot be found, an error is thrown and the user should supply `binned_outputs_dir` explicitly.

createGiottoVisiumHDObjectCell(
  segmented_outputs_dir,
  load_expression = TRUE,
  load_polygons = c("cell", "nucleus"),
  graphclust_annotated = FALSE,
  load_image = TRUE,
  load_transcripts = FALSE,
  binned_outputs_dir = NULL,
  micron = FALSE,
  barcodes = NULL,
  expression_source = "raw",
  feature_id_type = c("symbol", "ensembl"),
  expression_remove_zero_rows = TRUE,
  expression_split_by_type = TRUE,
  image_type = "hires",
  scalefactors_path = NULL,
  expression_path = NULL,
  image_path = NULL,
  geojson_path = NULL,
  instructions = NULL,
  verbose = NULL
)

Arguments

segmented_outputs_dir

filepath to the VisiumHD `segmented_outputs` directory.

load_expression

logical. Whether to load expression matrix.

load_polygons

character. Which polygon types to load. One or both of `"cell"` and `"nucleus"`. Set to `NULL` or `character(0)` to skip.

graphclust_annotated

logical. Whether to load graphclust-annotated polygon variants.

load_image

logical. Whether to load the paired image.

load_transcripts

logical. Whether to load 2 µm bin data as transcripts. Very memory expensive. Requires access to the `binned_outputs` directory (auto-detected or supplied via `binned_outputs_dir`).

binned_outputs_dir

(optional) filepath to the VisiumHD `binned_outputs` directory. Only needed when `load_transcripts = TRUE` and auto-detection of the sibling `binned_outputs` folder fails.

micron

logical. Set `TRUE` to load in micron scale.

barcodes

character. Specific cell barcodes to keep.

expression_source

character. One of `"raw"` or `"filtered"`.

feature_id_type

character. One of `"symbol"` or `"ensembl"`.

expression_remove_zero_rows

logical (default `TRUE`). Whether to remove features with no detections.

expression_split_by_type

logical (default `TRUE`). Whether to split expression by feature type.

image_type

character. One of `"hires"` (default) or `"lowres"`.

scalefactors_path

(optional) filepath to `scalefactors_json.json`.

expression_path

(optional) filepath to .h5 or matrix market directory.

image_path

(optional) filepath to image to use.

geojson_path

(optional) filepath or directory for polygon `.geojson` files.

instructions

giotto instructions to apply.

verbose

verbosity

Value

giotto object

See also

[importVisiumHD()] [createGiottoVisiumHDObjectBin()]

Examples

if (FALSE) {
seg_dir <- "path/to/visiumhd/segmented_outputs"
g <- createGiottoVisiumHDObjectCell(seg_dir)

# with transcript loading (auto-detects ../binned_outputs/)
g <- createGiottoVisiumHDObjectCell(seg_dir, load_transcripts = TRUE)

# with explicit binned_outputs path
g <- createGiottoVisiumHDObjectCell(seg_dir,
    load_transcripts = TRUE,
    binned_outputs_dir = "path/to/visiumhd/binned_outputs"
)
}