plotDimReduceModule {celda} | R Documentation |
Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimension reduction tool. The cells are colored by the module probability.
plotDimReduceModule( x, reducedDimName, useAssay = "counts", altExpName = "featureSubset", celdaMod, modules = NULL, dim1 = NULL, dim2 = NULL, size = 0.5, xlab = NULL, ylab = NULL, rescale = TRUE, limits = c(0, 1), colorLow = "grey90", colorHigh = "firebrick1", ncol = NULL, decreasing = FALSE ) ## S4 method for signature 'SingleCellExperiment' plotDimReduceModule( x, reducedDimName, useAssay = "counts", altExpName = "featureSubset", modules = NULL, dim1 = 1, dim2 = 2, size = 0.5, xlab = NULL, ylab = NULL, rescale = TRUE, limits = c(0, 1), colorLow = "grey90", colorHigh = "firebrick1", ncol = NULL, decreasing = FALSE ) ## S4 method for signature 'ANY' plotDimReduceModule( x, celdaMod, modules = NULL, dim1, dim2, size = 0.5, xlab = "Dimension_1", ylab = "Dimension_2", rescale = TRUE, limits = c(0, 1), colorLow = "grey90", colorHigh = "firebrick1", ncol = 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
|
useAssay |
A string specifying which assay
slot to use if |
altExpName |
The name for the altExp slot to use. Default "featureSubset". |
celdaMod |
Celda object of class "celda_G" or "celda_CG". Used only if
|
modules |
Character vector. Module(s) from celda model to be plotted. e.g. c("1", "2"). |
dim1 |
Integer or numeric vector. If |
dim2 |
Integer or numeric vector. If |
size |
Numeric. Sets size of point on plot. Default 0.5. |
xlab |
Character vector. Label for the x-axis. Default "Dimension_1". |
ylab |
Character vector. Label for the y-axis. Default "Dimension_2". |
rescale |
Logical. Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE. |
limits |
Passed to scale_colour_gradient. 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. |
colorHigh |
Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. |
ncol |
Integer. Passed to facet_wrap. Specify the number of columns for facet wrap. |
decreasing |
logical. Specifies the order of plotting the points.
If |
The plot as a ggplot object
data(sceCeldaCG) sce <- celdaTsne(sceCeldaCG) plotDimReduceModule(x = sce, reducedDimName = "celda_tSNE", modules = c("1", "2")) library(SingleCellExperiment) data(sceCeldaCG, celdaCGMod) sce <- celdaTsne(sceCeldaCG) plotDimReduceModule(x = counts(sce), dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1], dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2], celdaMod = celdaCGMod, modules = c("1", "2"))