Computes an HTML report from the Seurat workflow and returns the output SCE
object with the computations stored in it.
seuratReport(
inSCE,
outputFile = NULL,
outputDir = NULL,
subtitle = "BUMC Single Cell Sequencing Core",
authors = "Tianmu (Timo) Hu, Irzam Sarfraz",
sce = NULL,
biological.group = NULL,
phenotype.groups = NULL,
selected.markers = NULL,
clustering.resolution = 0.8,
variable.features = 2000,
pc.count = 10,
showSession = TRUE,
pdf = TRUE
)
Arguments
inSCE |
Input SingleCellExperiment object. |
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 . |
outputDir |
Specify the name of the output directory to save the
rendered HTML file. If NULL the file is stored to the current
working directory. |
subtitle |
A character value specifying the subtitle to use in the
Seurat report. |
authors |
A character value specifying the names of the authors
to use in the Seurat report. |
sce |
A character value specifying the path of the 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 differential expression 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 specifying the user decided
gene symbols of pre-selected markers that be used to generate gene plots in
addition to the gene markers computed from differential expression. |
clustering.resolution |
A numeric value indicating the resolution
to use with clustering. Default is 0.8 . |
variable.features |
A numeric value indicating the number of
top variable genes to identify in the seurat report. Default is 2000 . |
pc.count |
A numeric value indicating the number of principal
components to use in the analysis workflow. Default is 10 . |
showSession |
A logical value indicating if session information
should be displayed or not. Default is TRUE . |
pdf |
A logical value indicating if a pdf should also be
generated for each figure in the report. Default is TRUE . |
Value
A SingleCellExperiment
object that has the seurat computations
stored and can be used to interactively visualize the plots by importing
in the singleCellTK
user interface.