plotDimReduceGrid {celda} | R Documentation |
Creates a scatterplot given two dimensions from a data dimension reduction tool (e.g tSNE) output.
plotDimReduceGrid( x, reducedDimName, dim1 = NULL, dim2 = NULL, useAssay = "counts", altExpName = "featureSubset", size = 1, xlab = "Dimension_1", ylab = "Dimension_2", limits = c(-2, 2), colorLow = "blue4", colorMid = "grey90", colorHigh = "firebrick1", midpoint = 0, varLabel = NULL, ncol = NULL, headers = NULL, decreasing = FALSE ) ## S4 method for signature 'SingleCellExperiment' plotDimReduceGrid( x, reducedDimName, dim1 = NULL, dim2 = NULL, useAssay = "counts", altExpName = "featureSubset", size = 1, xlab = "Dimension_1", ylab = "Dimension_2", limits = c(-2, 2), colorLow = "blue4", colorMid = "grey90", colorHigh = "firebrick1", midpoint = 0, varLabel = NULL, ncol = NULL, headers = NULL, decreasing = FALSE ) ## S4 method for signature 'ANY' plotDimReduceGrid( x, dim1, dim2, size = 1, xlab = "Dimension_1", ylab = "Dimension_2", limits = c(-2, 2), colorLow = "blue4", colorMid = "grey90", colorHigh = "firebrick1", midpoint = 0, varLabel = NULL, ncol = NULL, headers = NULL, decreasing = FALSE )
x |
Numeric matrix or a SingleCellExperiment object
with the matrix located in the assay slot under |
reducedDimName |
The name of the dimension reduction slot in
|
dim1 |
Numeric vector. Second dimension from data dimension reduction output. |
dim2 |
Numeric vector. Second dimension from data dimension reduction output. |
useAssay |
A string specifying which assay
slot to use if |
altExpName |
The name for the altExp slot to use. Default "featureSubset". |
size |
Numeric. Sets size of point on plot. Default 1. |
xlab |
Character vector. Label for the x-axis. Default 'Dimension_1'. |
ylab |
Character vector. Label for the y-axis. Default 'Dimension_2'. |
limits |
Passed to scale_colour_gradient2. The range of color scale. |
colorLow |
Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. Default "blue4". |
colorMid |
Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. Default "grey90". |
colorHigh |
Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default "firebrick1". |
midpoint |
Numeric. The value indicating the midpoint of the
diverging color scheme. If |
varLabel |
Character vector. Title for the color legend. |
ncol |
Integer. Passed to facet_wrap. Specify the number of columns for facet wrap. |
headers |
Character vector. If 'NULL', the corresponding rownames are used as labels. Otherwise, these headers are used to label the genes. |
decreasing |
logical. Specifies the order of plotting the points.
If |
The plot as a ggplot object
data(sceCeldaCG) sce <- celdaTsne(sceCeldaCG) plotDimReduceGrid(x = sce, reducedDimName = "celda_tSNE", xlab = "Dimension1", ylab = "Dimension2", varLabel = "tSNE") library(SingleCellExperiment) data(sceCeldaCG) sce <- celdaTsne(sceCeldaCG) plotDimReduceGrid(x = counts(sce), dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1], dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2], xlab = "Dimension1", ylab = "Dimension2", varLabel = "tSNE")