plotTopHVG | R Documentation |
Plot highly variable genes
plotTopHVG(
inSCE,
method = "modelGeneVar",
hvgNumber = 2000,
useFeatureSubset = NULL,
labelsCount = 10,
featureDisplay = metadata(inSCE)$featureDisplay,
labelSize = 2,
dotSize = 2,
textSize = 12
)
inSCE |
Input |
method |
Select either |
hvgNumber |
Specify the number of top genes to highlight in red. Default
|
useFeatureSubset |
A character string for the |
labelsCount |
Specify the number of data points/genes to label. Should
be less than |
featureDisplay |
A character string for the |
labelSize |
Numeric, size of the text label on top HVGs. Default
|
dotSize |
Numeric, size of the dots of the features. Default |
textSize |
Numeric, size of the text of axis title, axis label, etc.
Default |
When hvgNumber = NULL
and useFeature = NULL
, only plot
the mean VS variance/dispersion scatter plot. When only hvgNumber
set,
label the top hvgNumber
HVGs ranked by the metrics calculated by
method
. When useFeatureSubset
set, label the features in
the subset on the scatter plot created with method
and ignore
hvgNumber
.
ggplot of HVG metrics and top HVG labels
runFeatureSelection
, runSeuratFindHVG
,
runModelGeneVar
, getTopHVG
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runModelGeneVar(mouseBrainSubsetSCE)
plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar")
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