featAssayPlotDefaults {iSEE} | R Documentation |
Create default settings for feature assay plot panels in the iSEE interface.
featAssayPlotDefaults(se, number)
se |
A SummarizedExperiment object. |
number |
An integer scalar, specifying the maximum number of feature assay plots that can be added to the interface. |
Parameters available to feature assay plots are:
YAxisFeatName
:Integer, the index of the feature for which to show the expression on the y-axis if YAxis="Feature name"
.
Defaults to 1, i.e., the first feature in se
.
Alternatively, a string can be supplied containing the name of the feature, i.e., the row name.
YAxisRowTable
:Character, what row statistics table should be used to choose a feature to display on the y-axis?
Any setting will override YAxisFeatName
with the selected row in the chosen table upon initialization of the app.
Defaults to "---"
, which means that no table will be used.
Assay
:Integer, which assay should be used to supply the expression values shown on the y-axis?
Defaults to 1, i.e., the first assay in se
.
Alternatively, a string can also be supplied containing the name of the assay, if assays(se)
has names.
XAxis
:Character, what type of variable should be shown on the x-axis?
Defaults to "None"
, but can also be "Row table"
, "Column data"
or "Feature name"
.
XAxisColData
:Character, what column of colData(se)
should be shown on the x-axis if XAxis="Column data"
?
Defaults to the first entry of colData(se)
.
XAxisFeatName
:Integer, the index of the feature for which to show the expression on the x-axis if XAxis="Feature name"
.
Defaults to 1, i.e., the first feature in se
.
Alternatively, a string can be supplied containing the name of the feature.
XAxisRowTable
:Character, which row statistic table should be used to choose a feature to put on the x-axis if XAxis="Row table"
?
Any setting will override XAxisFeatName
with the selected row in the chosen table upon initialization of the app.
Defaults to "---"
, which means that no table will be used.
All column-based parameters described in ?"iSEE point parameters"
are applicable.
All plot-based parameters described in ?"iSEE selection parameters"
are applicable.
A DataFrame containing default settings for parameters of each of number
feature assay panels.
Aaron Lun
?"iSEE point parameters"
,
?"iSEE selection parameters"
example(SingleCellExperiment, echo=FALSE) # mock up 'sce'. featAssayPlotDefaults(sce, n=1)