plotExpression {scater} | R Documentation |
Plot expression values for a set of features (e.g. genes or transcripts)
plotExpression(object, features, x = NULL, exprs_values = "logcounts", log2_values = FALSE, colour_by = NULL, shape_by = NULL, size_by = NULL, ncol = 2, xlab = NULL, show_median = FALSE, show_violin = TRUE, theme_size = 10, ...) plotExpressionDefault(object, aesth, ncol = 2, xlab = NULL, ylab = NULL, show_median = FALSE, show_violin = TRUE, show_smooth = FALSE, theme_size = 10, alpha = 0.6, size = NULL, scales = "fixed", one_facet = FALSE, se = TRUE, jitter = "swarm")
object |
an |
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 |
exprs_values |
character string indicating which values should be used
as the expression values for this plot. Valid arguments are |
log2_values |
should the expression values be transformed to the log2-scale for plotting (with an offset of 1 to avoid logging zeroes)? |
colour_by |
optional character string supplying name of a column of
|
shape_by |
optional character string supplying name of a column of
|
size_by |
optional character string supplying name of a column of
|
ncol |
number of columns to be used for the panels of the plot |
xlab |
label for x-axis; if |
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 |
theme_size |
numeric scalar giving default font size for plotting theme (default is 10) |
... |
optional arguments (from those listed above) passed to
|
aesth |
an |
ylab |
character string defining a label for the y-axis (y-axes) of 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. |
size |
numeric scalar optionally providing size for points if
|
scales |
character scalar, should scales be fixed ("fixed"),
free ("free"), or free in one dimension ("free_x"; "free_y", the default).
Passed to the |
one_facet |
logical, should expression values for features be plotted in one facet
instead of mutiple facets, one per feature? Default if |
se |
logical, should standard errors be shown (default |
jitter |
character scalar to define whether points are to be jittered
( |
Plot expression values (default log2(counts-per-million + 1), if available) for a set of features.
a ggplot plot object
## prepare data data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) example_sce <- calculateQCMetrics(example_sce) sizeFactors(example_sce) <- colSums(counts(example_sce)) example_sce <- normalize(example_sce) ## default plot plotExpression(example_sce, 1:15) plotExpression(example_sce, 1:15, jitter = "jitter") ## plot expression against an x-axis value plotExpression(example_sce, 1:6, "Mutation_Status") ## explore options plotExpression(example_sce, 1:6, x = "Mutation_Status", exprs_values = "logcounts", colour_by = "Cell_Cycle", show_violin = TRUE, show_median = TRUE) plotExpression(example_sce, 1:6, x = "Mutation_Status", exprs_values = "counts", colour_by = "Cell_Cycle", show_violin = TRUE, show_median = TRUE) plotExpression(example_sce, "Gene_0001", x = "Mutation_Status") plotExpression(example_sce, c("Gene_0001", "Gene_0004"), x="Mutation_Status") plotExpression(example_sce, "Gene_0001", x = "Gene_0002") plotExpression(example_sce, c("Gene_0001", "Gene_0004"), x="Gene_0002") ## plot expression against expression values for Gene_0004 plotExpression(example_sce, 1:4, "Gene_0004") plotExpression(example_sce, 1:4, "Gene_0004", show_smooth = TRUE) plotExpression(example_sce, 1:4, "Gene_0004", show_smooth = TRUE, se = FALSE)