Description Usage Arguments Value Examples
Plot results of reduced dimensions data of counts stored in any slot in the SingleCellExperiment object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | plotSCEScatter(
inSCE,
slot = NULL,
sample = NULL,
annotation,
feature = NULL,
groupBy = NULL,
shape = NULL,
reducedDimName = NULL,
conditionClass = NULL,
xlab = NULL,
ylab = NULL,
axisSize = 10,
axisLabelSize = 10,
dim1 = NULL,
dim2 = NULL,
bin = NULL,
binLabel = NULL,
dotSize = 2,
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
)
|
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required |
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. |
annotation |
Desired vector within the slot used for plotting. Default NULL. |
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. |
reducedDimName |
saved dimension reduction name in the SingleCellExperiment object. Required. |
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. Default is second PCA component for PCA data and NULL otherwise. |
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. |
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. |
a ggplot of the reduced dimensions.
1 2 3 4 5 | plotSCEScatter(
inSCE = mouseBrainSubsetSCE, legendTitle = NULL,
slot = "assays", annotation = "counts", feature = "Apoe",
reducedDimName = "TSNE_counts", labelClusters = FALSE
)
|
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