abyplots

Babyplots R Package

Babyplots is an easy to use library for creating interactive 3d graphs for exploring and presenting data.

Table of Contents

• Usage
• Plot types
  • Point cloud
  • Shape cloud
  • Surface
  • Heat map
  • Image stack
  • Mesh object
• The babyplots object

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Usage

The babyplots R package can be installed from its bitbucket page using devtools:

devtools::install_bitbucket("derpylz/babyplots.git")

And loaded in your R session with:

library(babyplots)

This will expose the six plotting functions:

pointCloud()
shapeCloud()
heatMap()
surface()
imgStack()
meshObject()

as well as the corresponding Shiny bindings

# pointCloud Shiny bindings:
pointCloudOutput()
renderPointCloud()
# shapeCloud Shiny bindings:
shapeCloudOutput()
renderShapeCloud()
# heatMap Shiny bindings:
heatMapOutput()
renderHeatmap()
# surface Shiny bindings:
surfaceOutput()
renderSurface()
# imgStack Shiny bindings:
imgStackOutput()
renderImgStack()
# meshObject Shiny bindings:
meshObjectOutput()
renderMeshObject()

You can remind yourself of the arguments to the plotting functions at any time using the R manual:

?pointCloud
?shapeCloud
?heatMap
?surface
?imgStack
?meshObject

You can create a simple plot using any of the plotting functions, which directly prints the resulting visualization. Alternatively, you can assign the return value of the plotting functions to a variable. This allows you to later change some of the properties of the resulting babyplots object, as well as to add additional plots to the visualization.

# surface plot of height data
surf1 <- surface(coordMatrix, "values", as.vector(t(coordMatrix)),
                 backgroundColor = "#dfdfdf", showUI = TRUE,
                 xScale = 0.1, yScale = 0.01, zScale = 0.1)
# the same height data, but flipped
surf2 <- surface(-coordMatrix, "values", as.vector(t(coordMatrix)), showLegend = FALSE)

surf1 + surf2

The following sections explain the plotting functions and the babyplots object in detail.

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Plot types

The following six plot types are currently available in the babyplots package. Each plotting function returns a babyplots object, which when printed into the console shows the visualization.

Point cloud

Point clouds are 3 dimensional scatter plots, where three variables (x, y and z) define the position of points in the coordinate system. One additional variable can be visualized by the color of the points.

The pointCloud() plotting function takes the following arguments:

Argument	Type	Default	Description
coords	matrix	required	3 column matrix with x, y and z coordinates.
colorBy	character	required	Controls how the colorVar values are interpreted. Either "categories" for discrete values, "values" for continuous values, or "direct" when colorVar is a vector of colors in hex format (e.g. "#e95420").
colorVar	character or numerical vector	required	Color variable for the data points, containing category names, numerical values, or hex color strings, depending on the colorBy parameter.
name	character	"point cloud"	Name of the plot for displaying it in a plot shape legend.
size	double	1	Point size
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
colorScale	character	NULL	Name of a colorbrewer scale (e.g. "OrRd"), "Viridis", or "custom". If set to "custom", the customColorScale parameter is also needed.
customColorScale	character vector	NULL	Character vector of at least 2 colors. Only needed if colorScale is set to "custom".
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
showLegend	logical	TRUE	Display legend for categories of values.
showShape	logical	FALSE	Add this plot to the legend of plot shapes.
fontSize	double	11	Size of legend text.
fontColor	character	"black"	Color of legend text. As a valid html color (e.g. "black" or "#000000").
legendTitle	character	""	Title for the legend
legendTitleFontSize	double	16	Size of the legend title font.
legendTitleFontColor	character	"black"	Color of the legend title font.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
hasAnimation	logical	FALSE	Show animation of 2D to 3D point cloud.
animationTargets	matrix	NULL	A 2D embedding of the 3D data to be used for the unfolding animation. 2 column matrix.
animationDelay	integer	100	Number of frames before animation from 2D to 3D is started.
animationDuration	integer	200	Number of frames for transitioning between 2D and 3D.
animationLoop	logical	FALSE	Loop the animation (forwards and reverse).
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
shapeLegendTitle	character	""	Title for the plot shape legend.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

Shape cloud

Shape clouds are 3 dimensional scatter plots, where three variables (x, y and z) define the position of 3-dimensional shapes in the coordinate system. One additional variable can be visualized by the color of the points.

Available shapes are:

• box
• sphere
• cylinder
• cone
• torus

All data points of one shapeCloud plot have the same shape. You can combine multiple shape plots with different shapes. If legendShowShape is set to TRUE, the plot will be listed in a separate legend, with its name and shape.

Additionally, each data point can have an information string assigned to it that is displayed when the corresponding shape in the plot is clicked. These strings can include line breaks ("\n").

The shapeCloud() plotting function takes the following arguments:

Argument	Type	Default	Description
coords	matrix	required	3 column matrix with x, y and z coordinates.
colorBy	character	required	Controls how the colorVar values are interpreted. Either "categories" for discrete values, "values" for continuous values, or "direct" when colorVar is a vector of colors in hex format (e.g. "#e95420").
colorVar	character or numerical vector	required	Color variable for the data points, containing category names, numerical values, or hex color strings, depending on the colorBy parameter.
name	character	"shape cloud"	Name of the plot for displaying it in a plot shape legend.
shape	character	"box"	Shape of the data points in the plot. One of c("box", "sphere", "torus", "cone", "cylinder").
size	double	1	Point size
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
colorScale	character	NULL	Name of a colorbrewer scale (e.g. "OrRd"), "Viridis", or "custom". If set to "custom", the customColorScale parameter is also needed.
customColorScale	character vector	NULL	Character vector of at least 2 colors. Only needed if colorScale is set to "custom".
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
showLegend	logical	TRUE	Display legend for categories of values.
showShape	logical	TRUE	Add this plot to the legend of plot shapes.
fontSize	double	11	Size of legend text.
fontColor	character	"black"	Color of legend text. As a valid html color (e.g. "black" or "#000000").
legendTitle	character	""	Title for the legend
legendTitleFontSize	double	16	Size of the legend title font.
legendTitleFontColor	character	"black"	Color of the legend title font.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
folded	logical	FALSE	Show animation of 2D to 3D point cloud.
foldedEmbedding	matrix	NULL	A 2D embedding of the 3D data to be used for the unfolding animation. 2 column matrix.
foldAnimDelay	integer	100	Number of frames before animation from 2D to 3D is started.
foldAnimDuration	integer	200	Number of frames for transitioning between 2D and 3D.
dpInfo	character vector	NULL	Vector with information to be displayed for each data point on click.
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
shapeLegendTitle	character	""	Title for the plot shape legend.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

Surface

The surface plot creates a 3 dimensional surface that is defined by a height variable for each point on a x-y plane given by the rows and columns of a 2d matrix. An additional variable can be visualized by the color of the surface points. The color is interpolated between the defined points of the surface.

The surface() plotting function takes the following arguments:

Argument	Type	Default	Description
coords	matrix	required	2-dimensional matrix with height data.
colorBy	character	required	Controls how the colorVar values are interpreted. Either "categories" for discrete values, "values" for continuous values, or "direct" when colorVar is a vector of colors in hex format (e.g. "#e95420").
colorVar	character or numerical vector	required	Color variable for the data points, containing category names, numerical values, or hex color strings, depending on the colorBy parameter.
name	character	"shape cloud"	Name of the plot for displaying it in a plot shape legend.
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
colorScale	character	NULL	Name of a colorbrewer scale (e.g. "OrRd"), "Viridis", or "custom". If set to "custom", the customColorScale parameter is also needed.
customColorScale	character vector	NULL	Character vector of at least 2 colors. Only needed if colorScale is set to "custom".
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
showLegend	logical	TRUE	Display legend for categories of values.
showShape	logical	FALSE	Add this plot to the legend of plot shapes.
fontSize	double	11	Size of legend text.
fontColor	character	"black"	Color of legend text. As a valid html color (e.g. "black" or "#000000").
legendTitle	character	""	Title for the legend
legendTitleFontSize	double	16	Size of the legend title font.
legendTitleFontColor	character	"black"	Color of the legend title font.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
shapeLegendTitle	character	""	Title for the plot shape legend.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

Heat map

The heat map is a 3 dimensional bar chart defined similarly to the surface plot, where the height of each bar on a x-y plane is given by the value in a row-column pair of a 2d matrix. An additional variable can be visualized by the color of the bar.

The heatMap() plotting function takes the following arguments:

Argument	Type	Default	Description
coords	matrix	required	2-dimensional matrix with height data.
colorBy	character	required	Controls how the colorVar values are interpreted. Either "categories" for discrete values, "values" for continuous values, or "direct" when colorVar is a vector of colors in hex format (e.g. "#e95420").
colorVar	character or numerical vector	required	Color variable for the data points, containing category names, numerical values, or hex color strings, depending on the colorBy parameter.
name	character	"shape cloud"	Name of the plot for displaying it in a plot shape legend.
size	double	1	Controls the width in the x and z dimensions of the pillars. Values should be between 0 and 1, values over 1 cause the pillars to intersect each other.
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
colorScale	character	NULL	Name of a colorbrewer scale (e.g. "OrRd"), "Viridis", or "custom". If set to "custom", the customColorScale parameter is also needed.
customColorScale	character vector	NULL	Character vector of at least 2 colors. Only needed if colorScale is set to "custom".
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
showLegend	logical	TRUE	Display legend for categories of values.
showShape	logical	FALSE	Add this plot to the legend of plot shapes.
fontSize	double	11	Size of legend text.
fontColor	character	"black"	Color of legend text. As a valid html color (e.g. "black" or "#000000").
legendTitle	character	""	Title for the legend
legendTitleFontSize	double	16	Size of the legend title font.
legendTitleFontColor	character	"black"	Color of the legend title font.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
folded	logical	FALSE	Show animation of 2D to 3D point cloud.
foldedEmbedding	matrix	NULL	A 2D embedding of the 3D data to be used for the unfolding animation. 2 column matrix.
foldAnimDelay	integer	100	Number of frames before animation from 2D to 3D is started.
foldAnimDuration	integer	200	Number of frames for transitioning between 2D and 3D.
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
shapeLegendTitle	character	""	Title for the plot shape legend.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

Image stack

The image stack visualizes a set of 2 dimensional slices with pixel values. The input is a tiff stack with rgb channels. It was created and optimized for fluorescent microscopy z-stack data and therefore works best with black background and bright signal.

The imgStack() plotting function takes the following arguments:

Argument	Type	Default	Description
img	character	required	Path to RGB tiff image stack.
size	double	1	Point size
threshold	double or list	0.1	Intensity threshold for background removal. Either one number (between 0 and 1) or list of numbers with threshold for each channel. (default 0.1).
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
intensityMode	character	"alpha"	Representation of pixel intensity, either "none", "alpha" or "mix". The default "alpha" generally looks best, but might be slightly slower than the other two options.
channelColors	list	list("#ff0000", "#00ff00", "#0000ff")	Set the colors for each of the channels, the default is for RGB images.
channelOpacities	list	list(1, 1, 1)	Set an overall opacity for each channel (default: list(1, 1, 1)). Only works together with intensityMode "alpha".
invertIntensities	logical	FALSE	Invert pixel intensity values. Set TRUE if image has dark foreground and light background. Inversion happens before thresholding.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

Mesh object

The meshObject visualizes a 3D model, or a scene of multiple 3D models from a glTF file.

The meshObject() plotting function takes the following arguments:

Argument	Type	Default	Description
filepath	character	required	Path to RGB glTF file.
meshScaling	list	list(1, 1, 1)	List of three numbers to scale the object(s) along the axes.
meshRotation	list	list(0, 0, 0)	List of three numbers to rotate the object(s) along the axes.
meshOffset	list	list(0, 0, 0)	List of three numbers to offset the position of the object(s) along the axes.
width	integer	NULL	Width of the widget, fits to the viewer pane when left empty.
height	integer	NULL	Height of the widget, fits to the viewer pane when left empty.
xScale	double	1	Scale x axis by a factor.
yScale	double	1	Scale y axis by a factor
zScale	double	1	Scale z axis by a factor
backgroundColor	character	"#ffffffff"	Color of background as hex color string.
showAxes	logical or list	FALSE	Display plot axes. Either one logical, or a list of three logicals, one for each axis (x, y, z).
axisLabels	list	list("X", "Y", "Z")	List of labels for the axes.
axisColors	character or list	"#666666"	Colors for the axes and their labels. Either one hex string (e.g. #000000), or a list of three hex strings, one for each axis (x, y, z).
tickBreaks	double or list	2	Interval of ticks on axes. Either one numerical value, or a list of three numbers, one for each axis (x, y, z).
showTickLines	logical, list or list of lists	FALSE	Display lines at tick intervals along axes. Either one logical, a list of three logicals, one for each axis (x, y, z), or a list of three lists with two logicals each, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
tickLineColors	character, list or list of lists	"#aaaaaa"	Colors for the tick lines. Either one hex string (e.g. #000000), a list of three strings, one for each axis (x, y, z), or a list of three lists with two strings, for each axis plane ([xy, xz], [yx, yz], [zx, zy]).
turntable	logical	FALSE	Rotate the camera around the plot.
rotationRate	double	0.01	Speed of turntable rotation. A positive value rotates the camera counter clockwise, a negative value clockwise.
upAxis	character	"+y"	Sets the camera up vector; Either "+x", "-x", "+y", "-y", "+z", or "-z".
showUI	logical	FALSE	Display buttons on the visualization. These buttons make it possible to add labels to the plot, or to export the plot as a JSON file.

---

The babyplots object

All plotting functions create a babyplots object. When printed to the console, this object shows the visualization. Assigning it to a variable allows you to change parameters of the visualization after its creation using the $ selector. The babyplots object has the following slots:

Slot	Type	Description
plots	list	A list of all plots that have been added to this babyplots object. The plots themselves are named lists, so their parameters that were set at the creation can also be accessed and changed through this slot.
turntable	logical	Controls the camera rotation around the plot
rotationRate	double	The speed at which the camera rotates around the plot, if turntable is set to TRUE
shapeLegendTitle	character	""	Title for the plot shape legend.
showUI	logical	Display buttons on the visualization.
backgroundColor	character	Color of background as hex color string.
xScale	double	Scale x axis by a factor.
yScale	double	Scale y axis by a factor
zScale	double	Scale z axis by a factor

Adding a two babyplots objects together creates a new babyplots object that contains both plots in the $plot slot. The general options (e.g. turntable, showUI, ...) are carried over from the first babyplots object.