Plot results of reduced dimensions data and colors by annotation data stored in the colData slot.
plotSCEDimReduceColData(
inSCE,
colorBy,
reducedDimName,
sample = NULL,
groupBy = NULL,
conditionClass = NULL,
shape = NULL,
xlab = NULL,
ylab = NULL,
baseSize = 12,
axisSize = NULL,
axisLabelSize = NULL,
dim1 = NULL,
dim2 = NULL,
bin = NULL,
binLabel = NULL,
dotSize = 0.5,
transparency = 1,
colorScale = NULL,
colorLow = "white",
colorMid = "gray",
colorHigh = "blue",
defaultTheme = TRUE,
title = NULL,
titleSize = 15,
labelClusters = TRUE,
clusterLabelSize = 3.5,
legendTitle = NULL,
legendTitleSize = NULL,
legendSize = NULL,
combinePlot = "none",
plotLabels = NULL
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
Color by a condition(any column of the annotation data). Required.
Saved dimension reduction matrix name in the SingleCellExperiment object. Required.
Character vector. Indicates which sample each cell belongs to.
Group by a condition(any column of the annotation data). Default NULL.
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.
Add shapes to each condition.
Character vector. Label for x-axis. Default NULL.
Character vector. Label for y-axis. Default NULL.
The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.
Size of x/y-axis ticks. Default NULL.
Size of x/y-axis labels. Default NULL.
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 0.5.
Transparency of the dots, values will be 0-1. Default 1.
Vector. Needs to be same length as the number of unique levels of colorBy. Will be used only if conditionClass = "factor" or "character". Default NULL.
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.
Logical. Whether the cluster labels are plotted.
Numeric. Determines the size of cluster label when `labelClusters` is set to TRUE. Default 3.5.
title of legend. Default NULL.
size of legend title. Default 12.
size of legend. Default NULL. Default FALSE.
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 coldata.
data("mouseBrainSubsetSCE")
plotSCEDimReduceColData(
inSCE = mouseBrainSubsetSCE, colorBy = "tissue",
shape = NULL, conditionClass = "factor",
reducedDimName = "TSNE_counts",
xlab = "tSNE1", ylab = "tSNE2", labelClusters = TRUE
)
plotSCEDimReduceColData(
inSCE = mouseBrainSubsetSCE, colorBy = "age",
shape = NULL, conditionClass = "numeric",
reducedDimName = "TSNE_counts", bin = c(-Inf, 20, 25, +Inf),
xlab = "tSNE1", ylab = "tSNE2", labelClusters = FALSE
)