Generates an HTML report for Seurat Run (including Normalization, Feature Selection, Dimensionality Reduction & Clustering) and returns the SCE object with the results computed and stored inside the object.

Generates an HTML report for Seurat Run (including Normalization, Feature Selection, Dimensionality Reduction & Clustering) and returns the SCE object with the results computed and stored inside the object.

reportSeuratRun(
  inSCE,
  biological.group = NULL,
  phenotype.groups = NULL,
  variable.features = 2000,
  pc.count = 50,
  runHVG = TRUE,
  plotHVG = TRUE,
  runDimRed = TRUE,
  plotJackStraw = FALSE,
  plotElbowPlot = TRUE,
  plotHeatmaps = TRUE,
  runClustering = TRUE,
  plotTSNE = TRUE,
  plotUMAP = TRUE,
  minResolution = 0.3,
  maxResolution = 1.5,
  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 tSNE & UMAP visualization.

phenotype.groups

A character value that specifies the name of the colData() column to use as additional phenotype variables in the Seurat report for tSNE & UMAP visualization.

variable.features

A numeric value indicating the number of top variable genes to identify in the report. Default is 2000.

pc.count

A numeric value indicating the number of principal components to use in the analysis workflow. Default is 50.

runHVG

A logical value indicating if feature selection should be run in the report. Default TRUE.

plotHVG

A logical value indicating if the top variable genes should be visualized through a mean-to-variance plot. Default is TRUE.

runDimRed

A logical value indicating if PCA should be computed in the report. Default is TRUE.

plotJackStraw

A logical value indicating if the JackStraw plot should be visualized for the principal components. Default is FALSE.

plotElbowPlot

A logical value indicating if the ElbowPlot should be visualized for the principal components. Default is FALSE.

plotHeatmaps

A logical value indicating if the Heatmaps should be visualized for the principal components. Default is FALSE.

runClustering

A logical value indicating if Clustering should be run over multiple resolutions as defined by the minResolution and maxResolution parameters. Default is TRUE.

plotTSNE

A logical value indicating if TSNE plot should be visualized for clusters. Default is TRUE.

plotUMAP

A logical value indicating if UMAP plot should be visualized for clusters. 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.

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.