plotDimReduceFeature {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 expression of the specified feature.
plotDimReduceFeature(x, ...) ## S4 method for signature 'SingleCellExperiment' plotDimReduceFeature( x, reducedDimName, dim1 = NULL, dim2 = NULL, useAssay = "counts", altExpName = "featureSubset", features, headers = NULL, normalize = FALSE, zscore = TRUE, exactMatch = TRUE, trim = c(-2, 2), limits = c(-2, 2), size = 1, xlab = "Dimension_1", ylab = "Dimension_2", colorLow = "blue4", colorMid = "grey90", colorHigh = "firebrick1", midpoint = 0, ncol = NULL, decreasing = FALSE ) ## S4 method for signature 'matrix' plotDimReduceFeature( x, dim1, dim2, features, headers = NULL, normalize = FALSE, zscore = TRUE, exactMatch = TRUE, trim = c(-2, 2), limits = c(-2, 2), size = 1, xlab = "Dimension_1", ylab = "Dimension_2", colorLow = "blue4", colorMid = "grey90", colorHigh = "firebrick1", midpoint = 0, ncol = NULL, decreasing = FALSE )
x |
Numeric matrix or a SingleCellExperiment object
with the matrix located in the assay slot under |
... |
Ignored. Placeholder to prevent check warning. |
reducedDimName |
The name of the dimension reduction slot in
|
dim1 |
Numeric vector. First 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". |
features |
Character vector. Features in the rownames of counts to plot. |
headers |
Character vector. If 'NULL', the corresponding rownames are used as labels. Otherwise, these headers are used to label the features. |
normalize |
Logical. Whether to normalize the columns of 'counts'.
Default |
zscore |
Logical. Whether to scale each feature to have a mean 0
and standard deviation of 1. Default |
exactMatch |
Logical. Whether an exact match or a partial match using
|
trim |
Numeric vector. Vector of length two that specifies the lower
and upper bounds for the data. This threshold is applied after row scaling.
Set to NULL to disable. Default |
limits |
Passed to scale_colour_gradient2. The range of color scale. |
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". |
colorLow |
Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. |
colorMid |
Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. |
colorHigh |
Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. |
midpoint |
Numeric. The value indicating the midpoint of the
diverging color scheme. If |
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) plotDimReduceFeature(x = sce, reducedDimName = "celda_tSNE", normalize = TRUE, features = c("Gene_99"), exactMatch = TRUE) library(SingleCellExperiment) data(sceCeldaCG) sce <- celdaTsne(sceCeldaCG) plotDimReduceFeature(x = counts(sce), dim1 = reducedDim(altExp(sce), "celda_tSNE")[, 1], dim2 = reducedDim(altExp(sce), "celda_tSNE")[, 2], normalize = TRUE, features = c("Gene_99"), exactMatch = TRUE)