scater (version 1.0.4)

plotExpression: Plot expression values for a set of features (e.g. genes or transcripts)

Description

Plot expression values for a set of features (e.g. genes or transcripts)

Usage

plotExpression(object, ...)
plotExpressionSCESet(object, features, x, exprs_values = "exprs", colour_by = NULL, shape_by = NULL, size_by = NULL, ncol = 2, xlab = NULL, show_median = FALSE, show_violin = TRUE, show_smooth = FALSE, theme_size = 10, log2_values = FALSE)
plotExpressionDefault(object, aesth, ncol = 2, xlab = NULL, ylab = NULL, show_median = FALSE, show_violin = TRUE, show_smooth = FALSE)
"plotExpression"(object, ...)
"plotExpression"(object, ...)

Arguments

object

an SCESet object containing expression values and experimental information. Must have been appropriately prepared. For the plotExpressionDefault method, the object argument is a data.frame in 'long' format providing expression values for a set of features to plot, plus metadata used in the aesth argument, but this is not meant to be a user-level operation.

...

optional arguments (from those listed above) passed to plotExpressionSCESet or plotExpressionDefault

features

a character vector of feature names or Boolean vector or numeric vector of indices indicating which features should have their expression values plotted

x

character string providing a column name of pData(object) or a feature name (i.e. gene or transcript) to plot on the x-axis in the expression plot(s). If a feature name, then expression values for the feature will be plotted on the x-axis for each subplot.

exprs_values

character string indicating which values should be used as the expression values for this plot. Valid arguments are "tpm" (default; transcripts per million), "norm_tpm" (normalised TPM values), "fpkm" (FPKM values), "norm_fpkm" (normalised FPKM values), "counts" (counts for each feature), "norm_counts", "cpm" (counts-per-million), "norm_cpm" (normalised counts-per-million), "exprs" (whatever is in the 'exprs' slot of the SCESet object; default), "norm_exprs" (normalised expression values) or "stand_exprs" (standardised expression values) or any other slots that have been added to the "assayData" slot by the user.

colour_by

optional character string supplying name of a column of pData(object) which will be used as a variable by which to colour expression values on the plot.

shape_by

optional character string supplying name of a column of pData(object) which will be used as a variable to define the shape of points for expression values on the plot.

size_by

optional character string supplying name of a column of pData(object) which will be used as a variable to define the size of points for expression values on the plot.

ncol

number of columns to be used for the panels of the plot

xlab

label for x-axis; if NULL (default), then x will be used as the x-axis label

show_median

logical, show the median for each group on the plot

show_violin

logical, show a violin plot for the distribution for each group on the plot

show_smooth

show a smoothed fit through the data points?

theme_size

numeric scalar giving default font size for plotting theme (default is 10)

log2_values

should the expression values be transformed to the log2-scale for plotting (with an offset of 1 to avoid logging zeroes)?

aesth

an aes object to use in the call to ggplot.

ylab

character string defining a label for the y-axis (y-axes) of the plot.

Value

a ggplot plot object

Details

Plot expression values (default log2(transcripts-per-million + 1), if available) for a set of features.

Examples

## prepare data
data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
example_sceset <- calculateQCMetrics(example_sceset)

## default plot
plotExpression(example_sceset, 1:6, "Mutation_Status")

## explore options
plotExpression(example_sceset, 1:6, x="Mutation_Status", exprs_values="exprs",
colour_by="Cell_Cycle", show_violin=TRUE, show_median=TRUE)
plotExpression(example_sceset, 1:6, x="Mutation_Status", exprs_values="counts",
colour_by="Cell_Cycle", show_violin=TRUE, show_median=TRUE)

## plot expression against expression values for Gene_0004
plotExpression(example_sceset, 1:4, "Gene_0004")
plotExpression(example_sceset, 1:4, "Gene_0004", show_smooth = TRUE)