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

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

reportSeurat(
  inSCE,
  biological.group = NULL,
  phenotype.groups = NULL,
  selected.markers = NULL,
  clustering.resolution = 0.8,
  variable.features = 2000,
  pc.count = 50,
  outputFile = NULL,
  outputPath = NULL,
  subtitle = NULL,
  authors = NULL,
  showSession = FALSE,
  pdf = FALSE,
  runHVG = TRUE,
  plotHVG = TRUE,
  runDimRed = TRUE,
  plotJackStraw = FALSE,
  plotElbowPlot = TRUE,
  plotHeatmaps = TRUE,
  runClustering = TRUE,
  plotTSNE = TRUE,
  plotUMAP = TRUE,
  minResolution = 0.3,
  maxResolution = 1.5,
  runMSClusters = TRUE,
  runMSBioGroup = TRUE,
  numTopFeatures = 10,
  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.

selected.markers

A character vector containing the user-specified gene symbols or feature names of marker genes that be used to generate gene plots in addition to the gene markers computed from differential expression.

clustering.resolution

A numeric value indicating the user-specified final resolution to use with clustering. Default is 0.8.

variable.features

A numeric value indicating the number of top variable features to identify. Default 2000.

pc.count

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

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.

runHVG

A logical value indicating if the feature selection computation should be run or not. Default is TRUE.

plotHVG

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

runDimRed

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

plotJackStraw

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

plotElbowPlot

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

plotHeatmaps

A logical value indicating if heatmaps should be plotted for the principal components. Default is TRUE.

runClustering

A logical value indicating if clustering section should be run in the report. Default is TRUE.

plotTSNE

A logical value indicating if TSNE plots should be visualized for clustering results. Default is TRUE.

plotUMAP

A logical value indicating if the UMAP plots should be visualized for the clustering results. Default is TRUE.

minResolution

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

maxResolution

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

runMSClusters

A logical value indicating if marker selection should be run between clusters. Default is TRUE.

runMSBioGroup

A logical value indicating if marker selection should be run between the biological.group parameter. Default is TRUE.

numTopFeatures

A numeric value indicating the number of top features to visualize in each group. Default 10.

forceRun

A logical value indicating if all algorithms should be re-run regardless if they have been computed previously in the input object. Default is TRUE.

Value

A SingleCellExperiment object with computations stored.