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

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Description

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

Usage

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plotExpression(object, ...)

plotExpressionSCESet(object, features, x = NULL, 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, alpha = 0.6, theme_size = 10,
  log2_values = FALSE, size = NULL, scales = "fixed", se = TRUE,
  jitter = "swarm")

plotExpressionDefault(object, aesth, ncol = 2, xlab = NULL, ylab = NULL,
  show_median = FALSE, show_violin = TRUE, show_smooth = FALSE,
  alpha = 0.6, size = NULL, scales = "fixed", one_facet = FALSE,
  se = TRUE, jitter = "swarm")

## S4 method for signature 'SCESet'
plotExpression(object, ...)

## S4 method for signature 'data.frame'
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

logical, show a smoothed fit through the expression values on the plot

alpha

numeric value between 0 (completely transparent) and 1 (completely solid) defining how transparent plotted points (cells) should be. Points are jittered horizontally if the x-axis value is categorical rather than numeric to avoid overplotting.

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)?

size

numeric scalar optionally providing size for points if size_by argument is not given. Default is NULL, in which case ggplot2 default is used.

scales

character scalar, should scales be fixed ("fixed"), free ("free"), or free in one dimension ("free_x"; "free_y", the default). Passed to the scales argument in the facet_wrap function from the ggplot2 package.

se

logical, should standard errors be shown (default TRUE) for the smoothed fit through the cells. (Ignored if show_smooth is FALSE).

jitter

character scalar to define whether points are to be jittered ("jitter") or presented in a "beeswarm" style (if "swarm"; default). "Beeswarm" style usually looks more attractive, but for datasets with a large number of cells, or for dense plots, the jitter option may work better.

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.

one_facet

logical, should expression values for features be plotted in one facet instead of mutiple facets, one per feature? Default if x = NULL.

Details

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

Value

a ggplot plot object

Examples

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## 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, 1:15)
plotExpression(example_sceset, 1:15, jitter = "jitter")

## plot expression against an x-axis value
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)
plotExpression(example_sceset, 1:4, "Gene_0004", show_smooth = TRUE, se = FALSE)

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