R/htmlReports.R
reportSeurat.Rd
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
)
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 numeric value indicating the user-specified
final resolution to use with clustering. Default is 0.8
.
A numeric value indicating the number of top
variable features to identify. Default 2000
.
A numeric value indicating the number of principal components
to use in the analysis workflow. Default is 50
.
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 the feature selection
computation should be run or not. Default is TRUE
.
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
.
A logical value indicating if PCA should be computed.
Default is TRUE
.
A logical value indicating if JackStraw plot be
visualized for the principal components. Default is FALSE
.
A logical value indicating if the ElbowPlot be
visualized for the principal components. Default is TRUE
.
A logical value indicating if heatmaps should be plotted
for the principal components. Default is TRUE
.
A logical value indicating if clustering section should
be run in the report. Default is TRUE
.
A logical value indicating if TSNE plots should be visualized
for clustering results. Default is TRUE
.
A logical value indicating if the UMAP plots should be
visualized for the clustering results. Default is TRUE
.
A numeric value indicating the minimum resolution to
use for clustering. Default is 0.3
.
A numeric value indicating the maximum resolution to use
for clustering. Default is 1.5
.
A logical value indicating if marker selection should
be run between clusters. Default is TRUE
.
A logical value indicating if marker selection should
be run between the biological.group
parameter.
Default is TRUE
.
A numeric value indicating the number of top features
to visualize in each group. Default 10
.
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
.
A SingleCellExperiment
object
with computations stored.