plotDeaLogFC | R Documentation |
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,
...
)
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. |
binwidth |
Numeric value. Denotes the binwidth to use for the histogram. |
clrp |
Character value. Specifies the color palette to be used to represent
groups of discrete variables. Run |
plot_type |
Character value. Specifies the type of plot to use to
visualize the results. If valid input options are not mentioned in the
description use |
limits_x |
Numeric vector of length two. Specify the limits of the x-axis. |
display_title |
Logical value. If set to TRUE an informative title is displayed. |
of_sample |
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.
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