sampAssayPlotDefaults {iSEE} | R Documentation |
Create default settings for sample assay plot panels in the iSEE interface.
sampAssayPlotDefaults(se, number)
se |
A SummarizedExperiment object. |
number |
An integer scalar, specifying the maximum number of sample assay plots that can be added to the interface. |
Parameters available to sample assay plots are:
YAxisSampName
:Integer, which column of se
should be shown on the y-axis?
Defaults to 1, i.e., the first column.
Alternatively, a character field can be supplied containing the name of the column.
YAxisColTable
:Character, what column statistics table should be used to choose a sample to display on the y-axis?
Any setting will override YAxisSampName
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 variable should be shown on the x-axis?
Defaults to "None"
, but can also be "Row data"
or "Sample name"
.
XAxisRowData
:Character, which column of rowData(se)
should be shown on the x-axis if XAxis="Row data"
?
Defaults to the first entry of rowData(se)
.
XAxisSampName
:Integer, which column of se
should be shown on the x-axis?
Defaults to 2 if se
contains multiple columns, otherwise it is set to 1.
Alternatively, a character field can be supplied containing the name of the column.
XAxisColTable
:Character, what column statistics table should be used to choose a sample to display on the x-axis, if XAxis="Sample name"
?
Any setting will override XAxisSampName
with the selected row in the chosen table upon initialization of the app.
Defaults to "---"
, which means that no table will be used.
All row-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
sample assay panels.
Charlotte Soneson
?"iSEE point parameters"
,
?"iSEE selection parameters"
example(SingleCellExperiment, echo=FALSE) # mock up 'sce'. sampAssayPlotDefaults(sce, n=1)