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 = 0.5, 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 0.5. |
| 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 )
