cluster_set_report: Create a report from a ClusterSet and Seurat object.

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Create a report from a ClusterSet and Seurat object.

Description

Create a report from a ClusterSet and Seurat object.

Usage

cluster_set_report(
  clusterset_object = NULL,
  seurat_object = NULL,
  file_path = NULL,
  force = FALSE,
  report_title = "Scigenex_report",
  report_author = "Unknown",
  heatmap_colors = colors_for_gradient("Ju1"),
  heatmap_color_ident = NULL,
  coord_flip = TRUE,
  pt_size = 2.75,
  go_info = c("ID", "Description", "GeneRatio", "pvalue", "qvalue", "Count"),
  verbosity = 1,
  pandoc_heap_size = "512m",
  report_id = rlang::hash(clusterset_object)
)

Arguments

clusterset_object	The ClusterSet object.
seurat_object	The Seurat object.
file_path	A file path where to store the report (html extension).
force	Whether to force erase output file.
report_title	A title for the report.
report_author	Names of report authors.
heatmap_colors	Colors for the heatmap gradient.
heatmap_color_ident	Colors for cell classes.
coord_flip	Whether to flip spatial coordinates.
pt_size	Size of the spots.
go_info	Info about GO stats. Should be from the list: "ONTOLOGY", "ID", "Description", "GeneRatio", "BgRatio", "pvalue", "p.adjust", "qvalue", "geneID", "Count"
verbosity	The verbosity level (0-3, defaut to 1.)
pandoc_heap_size	Fix the maximum memory used by pandoc. See https://pandoc.org/MANUAL.html.
report_id	Used to label code chunks.

Examples

# Load datasets
set_verbosity(3)
library(Seurat)
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
load_example_dataset("7870305/files/lymph_node_tiny_2")
# Create a report
cluster_set_report(clusterset_object = lymph_node_tiny_clusters_2[1,],
                   seurat_object=lymph_node_tiny_2,
                   pt_size=6)

dputhier/scigenex documentation built on Jan. 29, 2024, 3:40 p.m.