plotSasHeatmap.Rd
Plots gene expression changes against the distance to the spatial annotation using a heatmap.
plotSasHeatmap(
object,
variables,
ids = idSA(object),
distance = "dte",
resolution = recSgsRes(object),
core = FALSE,
arrange_rows = "none",
unit = getDefaultUnit(object),
bcs_exclude = character(0),
smooth_span = 0.3,
multiplier = 10,
clrsp = NULL,
border_linealpha = 0.75,
border_linecolor = "black",
border_linesize = 1,
border_linetype = "dashed",
.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 numeric variables to be included in the screening process. Makre sure that the correct matrix is active in the respective assays.
Character vector. Specifies the IDs of the spatial annotations of interest.
Distance measure
. Specifies
the distance from the border of the spatial annotation to the horizon in
the periphery up to which the screening is conducted. Defaults to a distance
that covers the whole tissue section the spatial annotation is located
on using distToEdge()
. (This distance must not be exceeded.)
Distance measure. The resolution
with which the expression gradient is inferred. Defaults are platform specific.
See more in detail section of recSgsRes()
.
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.
Character value containing the barcodes of observations to be excluded from the analysis.
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.
Given
to ggplot2::geom_vline()
. Adjusts appearance of the vertical line that
represents the border of the spatial annotation.
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.
The vignette on distance measures in SPATA2 has been replaced. Click
here
to read it.
library(SPATA2)
library(ggplot2)
data("example_data")
object <- example_data$object_UKF313T_diet
ids <- getSpatAnnIds(object, tags = c("necrotic", "compr"), test = "identical")
object <- normalizeCounts(object, activate = T)
# visualize with lines
plotSasLineplot(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
labs(x = "Distance to Necrosis")
# visualize with ridgeplots
plotSasRidgeplot(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
labs(x = "Distance to Necrosis")
# visualize with a heatmap
plotSasHeatmap(object, ids = ids, variables = c("VEGFA", "HM_HYPOXIA", "RCTM_TCR_SIGNALING", "CD74")) +
labs(x = "Distance to Necrosis")