4.2.1 What is a Scatterplot?
  4.2.2 Mouse Functions
  4.2.3 Main User Interface
      Master Scatterplot
      Cell Selector Scatterplot
  4.2.4 Scatterplot Properties
  4.2.5 Color Mapping

4.2.1 What is a Scatterplot?

PCX uses 2D and 3D scatter plots to examine the relationships in gene expression levels between two or three genes respectively. The coordinate axes of the graphs each represent the level of expression of a gene. Each data point plotted represents the expression level in a single cell of the embryo. The location of data points within the 2D of 3D plots, thus, shows the relative levels of expression in each cell for these genes whose expression is shown on the axes.

4.2.2 Mouse Functions:

Button(s)

Description

MOUSE L
  1.  Rotate the scatter plot (function only available in 3D scatter plots).

  2.  In each scatter plot-tab four scatter plots are displayed, three 2D scatter plots and the according 3D scatter plot. These four scatter plots are separated by split bars. Using the left mouse button these split-bars can be moved in order to resize the different scatter plots.

MOUSE L double click Aligns camera (function only available in 3D scatter plots).
MOUSE R

Move the scatter plot.

MOUSE R double click Centers the scatter plot.
MOUSE WHEEL

Zoom in and out.

SHIFT+MOUSE L

Redefine the Cell Selector by moving the entire Cell Selector-box or by just moving an edge or vertex of the Cell Selector-box. Which action is executed depends on the position of the mouse cursor relative to the position of the box defined by the Cell Selector.

CTRL+S

Save snapshot of the current scatter plot.

4.2.3 Main User Interface:

In PointCloudXplore the user can create several scatterplots for different gene combination. The different scatterplots are shown in tabs. In PointCloudXplore we distinguish between the Master Scatterplot and so called Cell Selector Scatterplots. The Master Scatterplot is used to define gene combinations to be viewed in a scatterplot and to create so called Data Cell Selectors which allow selection of cells in a scatteplot. The Cell Selector Scatterplots are responsible for the management and definition of Data Cell Selector. Each time a Data Cell Selector is created a new Cell Selector Scatterplot is defined in which the new Cell Selector can be edited. When a Data Cell Selector is deleted then the according Cell Selector Scatterplot is also closed while the Master Scatterplot is always shown. The Master- as well as Cell Selector Scatteplots tabs consist of a main menu and four scatterplots, three 2D scatterplots and the according 3D scatterplot. The split bars between the scatterplots are movable in order to resize the different plots. The functions and the main menu of the Master Scatterplot and Cell Selector Scatterplots are described below.

 

Name

Function
1 Master Scatterplot The first tab always contains the Master Scatterplot. The gene combination currently displayed in the Master Scatterplot is also shown in the title of the tab.
2 Cell Selector Scatterplots The remaining tabs contain so called "Cell Selector Scatterplots" while each of these scatterplots is responsible for the management of one Data Cell Selector.
3 2D Scatterplot Y/Z The top left viewer shows always a 2D scatterplot of the Y/Z gene dimension.
4 2D Scatterplot X/Z The top right viewer shows always a 2D scatterplot of the X/Z gene dimension.
5 2D Scatterplot X/Y The bottom left viewer shows always a 2D scatterplot of the X/Y gene dimension.
 6 3D Scatterplot X/Y/Z The bottom right viewer shows always the according 3D scatterplot of all 3 gene dimensions.
7 Horizontal Split Bar The horizontal split bar can be moved using Mouse-Left in order to define the size of the scatterplots shown in the top/bottom row of the window.
8 Vertical Split Bar (top) The top vertical split bar can be moved using Mouse-Left in order to define the size of the two top scatterplot viewers.
9 Vertical Splir Bar (bottom) The bottom vertical split bar can be moved using Mouse-Left in order to define the size of the two bottom scatterplot viewers.

Master Scatterplot:

The Master Scatterplot allows to define gene combinations of interest to be viewed in a scatterplot. As soon as a gene combination (three genes) has been selected it is possible to create a new Data Cell Selector (including a new Cell Selector Scatterplot) to perform data selection in the according plot. Beside this also the properties window, which is common for all scatterplots, can be accessed in the Master-Scatterplot. In the Master-Scatterplot all Cell Selectors currently displayed in the system are shown in the scatterplot.

Name

Function

1 Select X Select the gene dimension represented by the X-axis of the scatterplot. A pop-up window with the "Gene Selection Table"is shown. Each row in the "Gene Selection Table" represents one gene and each column one time-step. Select the gene to be displayed by checking the accoring check-boxes in the table and click "OK" to confirm the new selection.
2 Select Y Select the gene dimension represented by the Y-axis of the scatterplot. A pop-up window with the "Gene Selection Table"is shown. Each row in the "Gene Selection Table" represents one gene and each column one time-step. Select the gene to be displayed by checking the accoring check-boxes in the table and click "OK" to confirm the new selection.
3 Select Z Select the gene dimension represented by the Z-axis of the scatterplot. A pop-up window with the "Gene Selection Table"is shown. Each row in the "Gene Selection Table" represents one gene and each column one time-step. Select the gene to be displayed by checking the accoring check-boxes in the table and click "OK" to confirm the new selection.
4 Create Cell Selector Create a new Data Cell Selector for the current gene combination. The Create Cell Selector Window is shown in which the name and color of the new Cell Selector. After the user has confirmed creation of the Cell Selector by clicking the "Create Cell Selector" button in the Create Cell Selector Window, a new Cell Selector Scatterplot is also created which can then be used to edit main properties of and to define the new Cell Selector.
5 Properties Show the scatterplot properties window (see the Scatterplot Properties).
Cell Selector Scatterplot:

Each Cell Selector Scatterplot is responsible for the management of one Data Cell Selector. Basic properties of cell selectors, e.g. color, name and so on, can be edited in the main menu bar of the Cell Selector Scatterplots. When selecting a Cell Selector Scatterplot tab in the tab bar with the scatterplots the according Data Cell Selector is automatically set to be the Current Cell Selector. The cell selector can then be edited in the scatterplots. A Data Cell Selector selects cells based on their expression in three gene dimensions by defining an expression range for each gene. A Data Cell Selector defines in this way a 3D cube in N-Dimensional gene expression space. The selected cells are highlighted in the plot using color and the selected ranges are shown as rectangle (2D scatterplot) or as cube (3D scatterplot). In order to edit the cell selector it is possible to move a vertex or edge of the cell selector box, or the entire box itself by using Shift+Mouse Left ( see also the Scatterplot Controls).

Name Function
1 Scatterplot Name The name of a Cell Selector Scatterplot is composed as follows:

<Cell Selector Name> <(current)> <:> < gene Name 1 ,  gene Name2 , gene Name3 >

  1. Cell Selector Name: Name of the Cell Selector displayed in the Cell Selector Scatterplot
  2. (current): Optional string showing that this Cell Selector is the Current Cell Selector.
  3. Gene Names: Name of the genes the scatterplot (and Cell Selector) is defined for
2 Name Name of the Cell Selector. The name of the Cell Selector can be changed in the line edit.
3 Color Color of the Cell Selector. Click on the color label using Mouse left to open a color chooser in which the color of the Cell Selector can be redefined.
4 Brightness Change the brightness (display weight) of the Cell Selector by moving the slider
5 Display Define if the Cell Selector should be displayed in other views or not. If the Cell Selector is the current Cell Selector then the cell selector will still be displayed in all other views until another Cell Selector is set to be the current one.
6 Info String String with information about the Cell Selector. The string is composed as follows:

<% of Cells> <selected range X> <selected range Y> <selected range Z>

  1. % of Cells: The percentage of cells selected by the Cell Selector
  2. Selected range X: Selected gene expression range along the X-axis (red)
  3. Selected range Y: Selected gene expression range along the Y-axis (green)
  4. Selected range Z: Selected gene expression range along the Z-axis (blue)
7 Delete Delete the Cell Selector managed here. The "Cell Selector Scatterplot" is also deleted.

4.2.4 Scatterplot Properties:

The properties defined the scatterplot properties window are global options, i.e. they apply to all scatter plots.

Group Property  
Point Properties Size Define the radius of data points in the scatter plots.
  Opacity Define the opacity of data points in the scatter plots.
Halo Properties Size Define the size of halos. Halo-size should always be larger then the point size because otherwise the halos will not be visible.
  Opacity Define the opacity of halos. The halo-opacity should in general be set to a smaller value then the opacity of normal data  points.
Depth Clues Min-Gray Minimum gray value of not selected data points (see also the Color Mapping).
  Max-Gray Maximum gray value of not selected data points. (see also the Color Mapping).
  Min-Saturation Minimum saturation value for selected data points. If depth clues should only be used for not selected data points then this value should be set to 1.0.
Options Enable Halos Use halos. If halos are enabled then a blue ring is drawn around each data point similar to the corona of the sun. Halos make it easier to distinguish individual data points.
  Enable Alpha Shading Use transparent data points (and halos).
  Enable Depth Clues Use depth clues. If depth clues are enabled then points are colored according to the distance to the user. The gray value of not selected data points is varied so that close points are drawn with the according maximum gray value and far points are drawn in the darker minimum gray value. For selected data points the saturation can be varied. Selected points which are close to the user are drawn with full saturation while the saturation of color is lowered for points with a higher distance to the user. Depth clues do not only improve the view in a 3D scatter plot by providing a notion of depth  but in 2D plots the third displayed dimension is visible as color.
  Show all Cell Selectors in Cell Selector scatterplots For the "Cell Selector Scatterplots" one can decide if only the Cell Selector that is managed by the according scatterplot should be displayed there or if all Cell Selectors that are currently displayed in system should be shown. In the "Master-Scatterplot" all displayed Cell Selectors are always shown.
General Background Color Click on the Background Color button do open a color chooser to define the background color to be used in all scatter-plots.
Aspect Ratio Define the length of the X x Y x Z axes, and in this way the aspect ratio of all scatter-plots, using the three line edit boxes.

4.2.5 Color Mapping:

The color mapping in scatterplots is quite simple. In the basic color mapping all points not selected by any displayed Cell Selector are shown in white and all points selected by Cell Selectors are colored according to basic color (and display weight) of the Cell Selector defined by the user. If one point is selected by several Cell Selectors then the according colors are added up while the different color values are first multiplied with the according Cell Selector display weight.In the GUI of PointCloudXplore the display weight is in general termed "brightness" and can be set up using a simple slider.

If depth clues are enabled then the brightness of non selected points is lowered according to the distance to user. The user can here define a minimum- as well as a maximum gray value i.e. the gray color of not selected points is varied within the range of these two gray values. Close points are shown with the maximum gray and far points are drawn in the minimum gray. For selected data points the saturation of color can is varied according to the distance to the user when depth clues are enabled while the user can define the minimum saturation value for selected data points. By default this option is disabled by setting the minimum saturation value to 1.0 (full saturation). In 2D scatterplots the third axis shows always in direction to the user i.e. if depth clues are enabled then the values along the third axis are shown via color. In 2D scatterplots points with high values along the third axis are shown in the brighter maximum gray and points with low values along the third axis are shown in the darker minimum gray.