scatterplot.Rd
Renders a component containing a scatterplot with optional selection options
scatterplot(dashboard, object, ...) # S4 method for i2dashboard,missing scatterplot( dashboard, x, y, colour_by = NULL, labels = NULL, exprs_values = NULL, title = NULL, x_title = NULL, y_title = NULL, plot_title = NULL, source = "A", transmitter = NULL ) # S4 method for i2dashboard,SingleCellExperiment scatterplot( dashboard, object, from = c("colData", "rowData", "reducedDim"), x = NULL, y = NULL, colour_by = NULL, use_dimred = NULL, exprs_values = NULL, subset_row = NULL, ... ) # S4 method for i2dashboard,Seurat scatterplot( dashboard, object, from = c("meta.data", "meta.features", "embedding"), x = NULL, y = NULL, colour_by = NULL, use_dimred = NULL, assay = "RNA", slot = NULL, subset_row = NULL, ... )
dashboard | An object of class i2dashboard. |
---|---|
object | An object of class Seurat or SingleCellExperiment. |
... | Further parameters passed to the core function. |
x | Data that will be mapped to the x-axis (see Details). |
y | Data that will be mapped to the y-axis (see Details). |
colour_by | Numeric or factorial values that will be used for colouring. |
labels | An optional vector with sample names. A dropdown menu for colouring by label will be provided. |
exprs_values | Expression data of features of interest in rows and samples in columns (see Details). |
title | The title of the components junk. |
x_title | An optional title of the x-axis. If not provided the column names from |
y_title | An optional title of the y-axis. If not provided the column names from |
plot_title | An optional title of the plot. |
source | A character defining the id used in plotly's source argument of the component. |
transmitter | A character defining the id of an existing transmitter to obtain the data from. |
from | A character specifying where to obtain the data from |
use_dimred | A character vector indicating the reduced dimension to use from |
subset_row | An optional character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use. The default of NULL will use all features. |
assay | A character defining the assay of |
slot | A character defining the data slot of |
A string containing markdown code for the rendered component
The parameters x
, y
, colour_by
, use_dimred
, exprs_values
, assay
and slot
) take different arguments depending on the class of object
.
In case the i2dashboard,missing-method, the parameters x
, y
, colour_by
and exprs_values
are expected to be of class data.frame
or matrix
. The parameters x
, y
can also be numeric vectors. The parameters from
, use_dimred
, assay
and slot
can be ignored.
In case the i2dashboard,SingleCellExperiment-method, the parameters are expected to be of class character
:
the parameter from
can be either "colData"
, "rowData"
or "reducedDim"
use_dimred
the name of an item in reducedDims(object)
exprs_values
a valid assay name from assayNames(object)
In case of the i2dashboard,Seurat-method, the parameters are expected to be of class character
:
the parameter from
can be either "meta.data"
for sample metadata, "meta.feature"
for feature metadata, "embedding"
for a dimension reduction
reduction
the name of an item in object@reductions
assay
a valid assay name from names(object@assays)
slot
a valid data slot from assay
In both cases, x
, y
, colour_by
take column names of from
.