Trajectory analysis - mono_color

Development and data analysis: Haniffa Lab
Instructions:
  • This portal contains 4 option menus and 2 plotting areas;
  • The options menus are: "Visualisation options", "Colour by:", "Gene expression options", "Cell types:";
  • The plotting areas are: 1) the 3D viewer for difussion map coordinates (lower left) and 2) gene expression levels vs pseudotime (lower right and only visible if "Colour by" is set to "Gene")
  • Click on the 3D viewer area to rotate the object;
  • The visualisation options menu allows the user to set graphics parameters for the 3D viewer
  • The "Colour by:" menu is used to set by what criterion to color the data points in the 3D viewer. These are "Cell type", "Pseudotime" and "Gene";
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  • The "Gene expression options" menu is only functional if the option "Gene" is selected in the menu "Colour by:"
  • In the "Gene expression options" menu the user can select the gene which expression is shown both in the 3D viewer and in the gene expression by pseudotime plot;
  • Gene id can be selected from a drop-down menu or manually typed in the text box right of the drop-down menu;
  • Gene expression can be plotted as it is or min-max normalized. The first approach allows the user the gauge the scale of gene expression and the second approch allows for better visualisation of the changes in gene expression with pseudotime
Visualisation options





Colour by:


Gene expression options Or type here
Gene expression as:



Cell types: