R/htmlReports.R
reportSeuratMarkerSelection.Rd
Generates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object.
reportSeuratMarkerSelection(
inSCE,
biological.group = NULL,
phenotype.groups = NULL,
selected.markers = NULL,
runMarkerSelection = TRUE,
plotMarkerSelection = TRUE,
numTopFeatures = 10,
outputFile = NULL,
outputPath = NULL,
subtitle = NULL,
authors = NULL,
showSession = FALSE,
pdf = FALSE
)
Input SingleCellExperiment
object.
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.
A character vector that specifies the names of the
colData()
columns to use for differential expression in addition to
the biological.group
parameter.
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.
A logical value indicating if the marker selection
computation should be run or not. Default TRUE
.
A logical value indicating if the gene marker
plots should be visualized or not. Default TRUE
.
A numeric value indicating the number of top features
to visualize in each group. Default 10
.
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 SingleCellExperiment
object
with computations stored.