plotDeaPvalues.Rd
Use argument across
to specify the grouping
variable of interest across which the de-analysis has been conducted.
Valid input options for plot_type
are 'density' and
'histogram'.
plotDeaLogFC(
object,
across = NULL,
across_subset = NULL,
relevel = NULL,
method_de = NULL,
max_adj_pval = NULL,
binwidth = NULL,
clrp = NULL,
plot_type = "histogram",
scales = NULL,
limits_x = c(NA, NA),
display_title = NULL,
of_sample = NA,
...
)
plotDeaPvalues(
object,
across = NULL,
across_subset = NULL,
relevel = NULL,
method_de = NULL,
max_adj_pval = NULL,
binwidth = NULL,
clrp = NULL,
plot_type = "histogram",
scales = NULL,
limits_x = c(NA, NA),
display_title = NULL,
of_sample = NA,
...
)
An object of class spata2
.
Character value or NULL. Specifies the grouping variable of interest.
Use getGroupingOptions()
to obtain all variable names that group the
barcode spots of your object in a certain manner.
Character vector or NULL. Specifies the particular groups
of interest the grouping variable specified in argument across
contains.
If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.)
Use getGroupNames()
to obtain all valid input options.
Logical value. If set to TRUE the input order of across_subset
determines the order in which the groups of interest are displayed. Groups that
are not included are dropped which affects the colors with which they are displayed.
Character value. Denotes the method to according to which the de-analysis is performed.
Given to argument test.use
of the Seurat::FindAllMarkers()
-function. Run SPATA::dea_methods
to obtain all valid input options.
Numeric value. Sets the threshold for adjusted p-values. All genes with adjusted p-values above that threshold are ignored.
Numeric value. Denotes the binwidth to use for the histogram.
Character value. Specifies the color palette to be used to represent
groups of discrete variables. Run validColorPalettes()
to obtain valid
input options.
Character value. Specifies the type of plot to use to
visualize the results. If valid input options are not mentioned in the
description use validPlotTypess()
to obtain all valid input options.
Numeric vector of length two. Specify the limits of the x-axis.
Logical value. If set to TRUE an informative title is displayed.
This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.
Used to absorb deprecated arguments or functions.
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.