R/plot_dr.R
plotDimReduceModule.Rd
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 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 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"))