R/htmlReports.R
reportSeuratFeatureSelection.Rd
Generates an HTML report for Seurat Feature Selection and returns the SCE object with the results computed and stored inside the object.
reportSeuratFeatureSelection(
inSCE,
variable.features = 2000,
runHVG = TRUE,
plotHVG = TRUE,
outputFile = NULL,
outputPath = NULL,
subtitle = NULL,
authors = NULL,
showSession = FALSE,
pdf = FALSE,
forceRun = TRUE
)
Input SingleCellExperiment
object.
A numeric value indicating the number of top variable
features to identify. Default 2000
.
A logical value indicating if the feature selection algorithm
should be run or not. Default TRUE
.
A logical value indicating if the mean-to-variance plot
of the top variable feature should be visualized or not. Default TRUE
.
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
.
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
.
A character value specifying the subtitle to use in the
report. Default NULL
.
A character value specifying the names of the authors to use
in the report. Default NULL
.
A logical value indicating if session information
should be displayed or not. Default is FALSE
.
A logical value indicating if a pdf should also be generated for
each figure in the report. Default is FALSE
.
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
.
A SingleCellExperiment
object
with computations stored.