Plot results of reduced dimensions data and colors by feature data stored in the assays slot.
plotSCEDimReduceFeatures(
inSCE,
feature,
reducedDimName,
sample = NULL,
featureLocation = NULL,
featureDisplay = NULL,
shape = NULL,
useAssay = "logcounts",
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,
legendTitle = NULL,
legendSize = 10,
legendTitleSize = 12,
groupBy = NULL,
combinePlot = "none",
plotLabels = NULL
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
Name of feature stored in assay of SingleCellExperiment object.
saved dimension reduction name in the SingleCellExperiment object. Required.
Character vector. Indicates which sample each cell belongs to.
Indicates which column name of rowData to query gene.
Indicates which column name of rowData to use to display feature for visualization.
add shapes to each condition. Default NULL.
Indicate which assay to use. The default is "logcounts"
Character vector. Label for x-axis. Default NULL.
Character vector. Label for y-axis. Default NULL.
Size of x/y-axis ticks. Default 10.
Size of x/y-axis labels. Default 10.
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.
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.
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.
Character vector. Labels for the bins created by the `bin` parameter. Default NULL.
Size of dots. Default 0.1.
Transparency of the dots, values will be 0-1. Default 1.
Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.
Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.
Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.
adds grid to plot when TRUE. Default TRUE.
Title of plot. Default NULL.
Size of title of plot. Default 15.
title of legend. Default NULL.
size of legend. Default 10.
size of legend title. Default 12.
Facet wrap the scatterplot based on value.
Default NULL
.
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".
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.
a ggplot of the reduced dimension plot of feature data.
data("mouseBrainSubsetSCE")
plotSCEDimReduceFeatures(
inSCE = mouseBrainSubsetSCE, feature = "Apoe",
shape = NULL, reducedDimName = "TSNE_counts",
useAssay = "counts", xlab = "tSNE1", ylab = "tSNE2"
)