plotSCEDimReduceColData {singleCellTK} | R Documentation |
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 = 2, 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. |
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 2. |
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 )