plotDistributionAcross.Rd
Visualizes the distribution of values of a set of variables for the whole sample across specific subgroups.
plotDistributionAcross()
Takes the spata-object as the starting point and creates the
necessary data.frame from scratch according to additional parameters.
plotDistributionAcross2()
Takes a data.frame as the starting point.
plotDistributionAcross( object, of_sample = "", variables, across, across_subset = NULL, method_gs = "mean", plot_type = "violin", binwidth = 0.05, clrp = "milo", ..., normalize = TRUE, assign = FALSE, assign_name, verbose = TRUE ) plotDistributionAcross2( df, variables = "all", across, across_subset = NULL, plot_type = "violin", binwidth = 0.05, clrp = "milo", ..., normalize = TRUE, assign = FALSE, assign_name, verbose = TRUE )
object | A valid spata-object. |
---|---|
of_sample | The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen. |
variables | Character vector. The numeric variables of interest. |
across | Character value. The name of the discrete feature-variable of interest. Hint: Character- or factor- variables are discrete variables. These functionally assign the barcode spots to distinct
groups or clusters (e.g. segment or seurat_clusters) whoose properties you might want
to compare against each other. Use |
across_subset | Character vector or NULL. Specify the particular groups or clusters of interest the feature-variable
specified in argument Hint: Use |
method_gs | Character value. The method according to which gene sets will be handled
specified as a character of length one. This can be either 'mean' or one
of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to
|
plot_type | Character value. One of 'histogram', 'density', 'violin', 'boxplot' and 'ridgeplot'. |
binwidth | The binwidth to use if |
... | additional arguments to |
normalize | Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded. |
assign | Logical. If set to TRUE a named list will be assigned to the global environment. This list contains data and information to rebuild or additionally customize the output plot of this function. |
assign_name | The name the assigned list is supposed to have specified as a single character value. |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
df | A data.frame that contains the numeric variables specified in |