seuratReport {singleCellTK} | R Documentation

## Computes an HTML report from the Seurat workflow and returns the output SCE object with the computations stored in it.

### Description

Computes an HTML report from the Seurat workflow and returns the output SCE object with the computations stored in it.

### Usage

    seuratReport(
      inSCE,
      outputFile = NULL,
      outputDir = NULL,
      subtitle = "BUMC Single Cell Sequencing Core",
      authors = "Tianmu (Timo) Hu, Irzam Sarfraz",
      sce = NULL,
      biological.group = NULL,
      phenotype.groups = NULL,
      selected.markers = NULL,
      clustering.resolution = 0.8,
      variable.features = 2000,
      pc.count = 10,
      showSession = TRUE,
      pdf = TRUE
    )

### Arguments

`inSCE` | Input `SingleCellExperiment` object.
`outputFile` | Specify the name of the generated output HTML file. If `NULL` then the output file name will be based on the name of the Rmarkdown template. Default `NULL`.
`outputDir` | Specify the name of the output directory to save the rendered HTML file. If `NULL` the file is stored to the current working directory.
`subtitle` | A `character` value specifying the subtitle to use in the Seurat report.
`authors` | A `character` value specifying the names of the authors to use in the Seurat report.
`sce` | A `character` value specifying the path of the input `SingleCellExperiment` object.
`biological.group` | A character value that specifies the name of the `colData` column to use as the main biological group in the seurat report for differential expression and grouping.
`phenotype.groups` | A `character` vector that specifies the names of the `colData` columns to use for differential expression in addition to the `biological.group` parameter.
`selected.markers` | A `character` vector specifying the user decided gene symbols of pre-selected markers that be used to generate gene plots in addition to the gene markers computed from differential expression.
`clustering.resolution` | A `numeric` value indicating the resolution to use with clustering. Default is `0.8`.
`variable.features` | A `numeric` value indicating the number of top variable genes to identify in the seurat report. Default is `2000`.
`pc.count` | A `numeric` value indicating the number of principal components to use in the analysis workflow. Default is `10`.
`showSession` | A `logical` value indicating if session information should be displayed or not. Default is `TRUE`.
`pdf` | A `logical` value indicating if a pdf should also be generated for each figure in the report. Default is `TRUE`.

### Value

A `SingleCellExperiment` object that has the seurat computations stored and can be used to interactively visualize the plots by importing in the `singleCellTK` user interface.

[Package singleCellTK version 2.2.0 Index]