Usage
plotTSNE(object, ...)
"plotTSNE"(object, ntop = 500, ncomponents = 2, exprs_values = "exprs", colour_by = NULL, shape_by = NULL, size_by = NULL, feature_set = NULL, return_SCESet = FALSE, scale_features = TRUE, draw_plot = TRUE, theme_size = 10, rand_seed = NULL, perplexity = floor(ncol(object)/5), legend = "auto", ...)
Arguments
...
further arguments passed to Rtsne ntop
numeric scalar indicating the number of most variable features to
use for the t-SNE Default is 500, but any ntop argument is
overrided if the feature_set argument is non-NULL.
ncomponents
numeric scalar indicating the number of t-SNE
components to plot, starting from the first t-SNE component. Default is
2. If ncomponents is 2, then a scatterplot of component 1 vs component
2 is produced. If ncomponents is greater than 2, a pairs plots for the
top components is produced. NB: computing more than two components for t-SNE
can become very time consuming.
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 named element of the assayData slot of the SCESet
object that can be accessed with the get_exprs function.
colour_by
character string defining the column of pData(object) to
be used as a factor by which to colour the points in the plot.
shape_by
character string defining the column of pData(object) to
be used as a factor by which to define the shape of the points in the plot.
size_by
character string defining the column of pData(object) to
be used as a factor by which to define the size of points in the plot.
feature_set
character, numeric or logical vector indicating a set of
features to use for the t-SNE calculation. If character, entries must all be
in featureNames(object). If numeric, values are taken to be indices for
features. If logical, vector is used to index features and should have length
equal to nrow(object).
return_SCESet
logical, should the function return an SCESet
object with principal component values for cells in the
reducedDimension slot. Default is FALSE, in which case a
ggplot object is returned.
scale_features
logical, should the expression values be standardised
so that each feature has unit variance? Default is TRUE.
draw_plot
logical, should the plot be drawn on the current graphics
device? Only used if return_SCESet is TRUE, otherwise the plot
is always produced.
theme_size
numeric scalar giving default font size for plotting theme
(default is 10).
rand_seed
(optional) numeric scalar that can be passed to
set.seed to make plots reproducible.
perplexity
numeric scalar value defining the "perplexity parameter"
for the t-SNE plot. Passed to Rtsne - see documentation
for that package for more details. legend
character, specifying how the legend(s) be shown? Default is
"auto", which hides legends that have only one level and shows others.
Alternatives are "all" (show all legends) or "none" (hide all legends).