Plot results of reduced dimensions data of counts stored in any slot in the SingleCellExperiment object.
plotSCEScatter(
inSCE,
annotation,
reducedDimName = NULL,
slot = NULL,
sample = NULL,
feature = NULL,
groupBy = NULL,
shape = NULL,
conditionClass = NULL,
xlab = NULL,
ylab = NULL,
axisSize = 10,
axisLabelSize = 10,
dim1 = NULL,
dim2 = NULL,
bin = NULL,
binLabel = NULL,
dotSize = 0.1,
transparency = 1,
colorLow = "white",
colorMid = "gray",
colorHigh = "blue",
defaultTheme = TRUE,
title = NULL,
titleSize = 15,
labelClusters = TRUE,
legendTitle = NULL,
legendTitleSize = 12,
legendSize = 10,
combinePlot = "none",
plotLabels = NULL
)Arguments
- inSCE
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
- annotation
Desired vector within the slot used for plotting. Default NULL.
- reducedDimName
saved dimension reduction name in the SingleCellExperiment object.
- slot
Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Default NULL.
- sample
Character vector. Indicates which sample each cell belongs to.
- feature
name of feature stored in assay of SingleCellExperiment object. Will be used only if "assays" slot is chosen. Default NULL.
- groupBy
Group by a condition(any column of the annotation data). Default NULL.
- shape
add shapes to each condition.
- conditionClass
class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.
- xlab
Character vector. Label for x-axis. Default NULL.
- ylab
Character vector. Label for y-axis. Default NULL.
- axisSize
Size of x/y-axis ticks. Default 10.
- axisLabelSize
Size of x/y-axis labels. Default 10.
- dim1
1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
- dim2
2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
- bin
Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.
- binLabel
Character vector. Labels for the bins created by the `bin` parameter. Default NULL.
- dotSize
Size of dots. Default 0.1.
- transparency
Transparency of the dots, values will be 0-1. Default 1.
- colorLow
Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.
- colorMid
Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.
- colorHigh
Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.
- defaultTheme
adds grid to plot when TRUE. Default TRUE.
- title
Title of plot. Default NULL.
- titleSize
Size of title of plot. Default 15.
- labelClusters
Logical. Whether the cluster labels are plotted.
- legendTitle
title of legend. Default NULL.
- legendTitleSize
size of legend title. Default 12.
- legendSize
size of legend. Default 10.
- combinePlot
Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".
- plotLabels
labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.
Value
a ggplot of the reduced dimensions.
Examples
data("mouseBrainSubsetSCE")
plotSCEScatter(
inSCE = mouseBrainSubsetSCE, legendTitle = NULL,
slot = "assays", annotation = "counts", feature = "Apoe",
reducedDimName = "TSNE_counts", labelClusters = FALSE
)
