Generates an HTML report for Seurat Clustering and returns the SCE object with the results computed and stored inside the object.

Generates an HTML report for Seurat Clustering and returns the SCE object with the results computed and stored inside the object.

reportSeuratClustering(
  inSCE,
  biological.group = NULL,
  phenotype.groups = NULL,
  runClustering = TRUE,
  plotTSNE = TRUE,
  plotUMAP = TRUE,
  minResolution = 0.3,
  maxResolution = 1.5,
  numClusters = 10,
  significant_PC = 10,
  outputFile = NULL,
  outputPath = NULL,
  subtitle = NULL,
  authors = NULL,
  showSession = FALSE,
  pdf = FALSE,
  forceRun = TRUE
)

Arguments

inSCE

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 marker selection 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.

runClustering

A logical value indicating if Clustering should be run or not in the report. Default is TRUE. If FALSE, parameters plotTSNE and plotUMAP are also set to FALSE.

plotTSNE

A logical value indicating if TSNE plots should be visualized in the clustering section of the report. Default is TRUE.

plotUMAP

A logical value indicating if UMAP plots should be visualized in the clustering section of the report. Default is TRUE.

minResolution

A numeric value indicating the minimum resolution to use for clustering. Default 0.3.

maxResolution

A numeric value indicating the maximum resolution to use for clustering. Default 1.5.

numClusters

temp (to remove)

significant_PC

temp (change to pc.use)

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.

outputPath

Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

subtitle

A character value specifying the subtitle to use in the report. Default NULL.

authors

A character value specifying the names of the authors to use in the report. Default NULL.

showSession

A logical value indicating if session information should be displayed or not. Default is FALSE.

pdf

A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

forceRun

A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

Value

A SingleCellExperiment object with computations stored.