MicroArray ColoredScatterView

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==Overview==
 
==Overview==
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[[image:ScatterColorView.png]]
  
 
The ScatterColorView is a scatter plot, most often plotting coordinates from dimension reduction techniques such as tSNE or UMAP, colored by the genes intensity. It is available for -Omic /Microarray Data objects.
 
The ScatterColorView is a scatter plot, most often plotting coordinates from dimension reduction techniques such as tSNE or UMAP, colored by the genes intensity. It is available for -Omic /Microarray Data objects.

Latest revision as of 22:19, 14 January 2020

Contents

Overview

ScatterColorView.png

The ScatterColorView is a scatter plot, most often plotting coordinates from dimension reduction techniques such as tSNE or UMAP, colored by the genes intensity. It is available for -Omic /Microarray Data objects.

This View creates one plot per gene (row of an expression matrix), plotting the expression of this gene on the Y-axis for each cell/sample along the X-axis.

This View can be added by right-clicking an Omic data object and selecting Select View | ScatterColorView. Next step will ask for the coordinates to be used in the chart view. Coordinates must be saved in the Design table of the Omic data object.

ColoredScatterViewFlow.png


Commonly, a user will either import dimension reduction "clustering" results from a text file, or run an analysis such as tSNE in OmicSoft Studio. Follow these instructions to quickly move coordinates to your OmicData object.

Customizing This View

View Controller

You can read descriptions of all Options, or read about select options that are useful for this View.

Data

  • Specify Title Columns: For each plot of a row (gene), multiple column meta data from the Annotation table can be displayed as title.

Trellis

In addition to automatic trellising by Gene (row):

  • data can be subset by column metadata (for example to only view one cell type per plot)
  • plots can be subset by particular samples/cells (columns)

Properties

  • Change Chart Properties: Change details of the graph, X- and Y-axes, e.g. plot line thickness, rotate labels, etc.
  • Flip X/Y Axis: Rotate the plot.
  • Change Symbol Properties: If plotting data points (e.g. Scatter, BoxPlot), change how each point is drawn.
  • Specify Coordinates: Update coordinates used for plotting.

Customize

  • Change To Speed-First Mode: Switch to simplified shapes for computationally-efficient drawing of many points.

Export

  • Open in Editor: Open the underlying data for the current View in your Text Editor
  • Open in Excel: Open the underlying data for the current View in Excel

Filtering

The underlying expression matrix can be filtered by Variable or Observation metadata to control which genes or cells/samples are being displayed in the ColoredScatterView.

Oscript

View can be opened inside the Array Studio using the "AddView Procedure", or run through Oscripts to automate.


Begin AddView; 
Data MicroArrayData; 
Project 10K_PBMC; 
Type ScatterColorView /XAxis=V1 /YAxis=V2; 
Options /Opened=True /Selected=True; 
Name ColoredScatter2D_Script; 
End; 

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