plotStsHeatmap.Rd
Displays variable-expression values along a trajectory direction with a smoothed heatmap (from left to right).
plotStsHeatmap(
object,
variables,
id = idST(object),
width = getTrajectoryLength(object, id),
arrange_rows = "none",
unit = getDefaultUnit(object),
smooth_span = 0.3,
multiplier = 10,
clrsp = NULL,
.f = NULL,
.cols = dplyr::everything(),
verbose = NULL,
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Character vector. The names of the data variables of interest.
Alter the way the rows of the heatmap
are displayed in order to highlight patterns. Currently either 'maxima',
'minima' or 'input'. If 'input', variables are displayed
in the same order as they are provided in the argument variables
.
Character value. Specifies the desired unit in
which distance measures
or area measures are provided.
Run validUnitsOfLength()
or validUnitsOfArea()
for valid
input options.
Numeric value. Controls the degree of smoothing.
Given to argument span
of stats::loess()
.
Numeric value. For better visualization the transient pattern
is smoothed with a loess fit. The total number of predicted values (via stats::predict()
)
is the number of bins multiplied with the input for this argument.
Character value. Specifies the color spectrum to be used to represent
continuous values of numeric variables. Run validColorSpectra()
to obtain
valid input options.
Logical. If TRUE
, informative messages regarding
the computational progress will be printed.
(Warning messages will always be printed.)
Used to absorb deprecated arguments or functions.
A ggplot.
library(SPATA2)
data("example_data")
object <- example_data$object_UKF269T_diet
object <- normalizeCounts(object, activate = TRUE)
genes <- c("EGFR", "MBP", "MAG", "SNAP25")
plotStsHeatmap(object, id = "horizontal_mid", variables = genes)
plotStsLineplot(object, id = "horizontal_mid", variables = genes)
plotStsRidgeplot(object, id = "horizontal_mid", variables = genes)