plotDeaSummary | R Documentation |
This function is a wrapper around plotDeaPvalues(),
plotDeaLogFC()
and plotDeaGeneCount()
and returns
a combined ggplot. Set the respective argument to FALSE if
you want to skip one of the functions or specify their arguments
by providing a named list of arguments.
plotDeaSummary(
object,
across = NULL,
across_subset = NULL,
relevel = NULL,
method_de = NULL,
max_adj_pval = NULL,
clrp = NULL,
plotDeaGeneCount = list(display_title = TRUE),
plotDeaLogFC = list(display_title = FALSE),
plotDeaPvalues = list(display_title = FALSE),
verbose = NULL,
of_sample = NA
)
object |
An object of class |
across |
Character value or NULL. Specifies the grouping variable of interest. Use |
across_subset |
Character vector or NULL. Specifies the particular groups
of interest the grouping variable specified in argument 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 |
relevel |
Logical value. If set to TRUE the input order of |
method_de |
Character value. Denotes the method to according to which the de-analysis is performed.
Given to argument |
max_adj_pval |
Numeric value. Sets the threshold for adjusted p-values. All genes with adjusted p-values above that threshold are ignored. |
clrp |
Character value. Specifies the color palette to be used to represent
groups of discrete variables. Run |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
of_sample |
This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample. |
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.
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