R/htmlReports.R
reportSeuratRun.Rd
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
)
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 tSNE & UMAP visualization.
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.
A numeric value indicating the number of top
variable genes to identify in the report. Default is 2000
.
A numeric value indicating the number of principal
components to use in the analysis workflow. Default is 50
.
A logical value indicating if feature selection should be run
in the report. Default TRUE
.
A logical value indicating if the top variable genes should
be visualized through a mean-to-variance plot. Default is TRUE
.
A logical value indicating if PCA should be computed in the
report. Default is TRUE
.
A logical value indicating if the JackStraw plot should
be visualized for the principal components. Default is FALSE
.
A logical value indicating if the ElbowPlot should be
visualized for the principal components. Default is FALSE
.
A logical value indicating if the Heatmaps should be
visualized for the principal components. Default is FALSE
.
A logical value indicating if Clustering should be
run over multiple resolutions as defined by the minResolution
and
maxResolution
parameters. Default is TRUE
.
A logical value indicating if TSNE plot should be visualized
for clusters. Default is TRUE
.
A logical value indicating if UMAP plot should be visualized
for clusters. Default is TRUE
.
A numeric value indicating the minimum resolution to use
for clustering. Default 0.3
.
A numeric value indicating the maximum resolution to use
for clustering. Default 1.5
.
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.