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 )
inSCE | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required. |
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colorBy | Color by a condition(any column of the annotation data). Required. |
reducedDimName | Saved dimension reduction matrix name in the SingleCellExperiment object. Required. |
sample | Character vector. Indicates which sample each cell belongs to. |
groupBy | Group by a condition(any column of the annotation data). Default NULL. |
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. |
shape | Add shapes to each condition. |
xlab | Character vector. Label for x-axis. Default NULL. |
ylab | Character vector. Label for y-axis. Default NULL. |
baseSize | The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize. |
axisSize | Size of x/y-axis ticks. Default NULL. |
axisLabelSize | Size of x/y-axis labels. Default NULL. |
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 0.5. |
transparency | Transparency of the dots, values will be 0-1. Default 1. |
colorScale | 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. |
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. |
clusterLabelSize | Numeric. Determines the size of cluster label when `labelClusters` is set to TRUE. Default 3.5. |
legendTitle | title of legend. Default NULL. |
legendTitleSize | size of legend title. Default 12. |
legendSize | size of legend. Default NULL. Default FALSE. |
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. |
a ggplot of the reduced dimension plot of coldata.
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 )