VGAS Tutorials: RNA-Seq

RNA-Seq Plot Viewer (NEW)

Loading & Saving Data

Select the RNA-Seq option.
Load the data using one of the following two options:

OPTION 1: Loading from the Gene (.csv) and Metadata (.txt) files.
File -> Open, and select the Gene and Metadata files together.
Highlight these files in the left panel.
Double-click the 'RNA-Seq Plot Viewer' option in the right panel.
Select the cells in the top panel and add '+ button' to the bottom panel.

THEN EITHER
GENERATE UMAP - set the required UMAP options and click 'GENERATE R PLOT'. This may take a while to complete depending on the size of the data.
Once complete click 'GENERATE PLOT VIEWER'.
OR
SKIP PLOT - skips generating the UMAP plots, but allows the user to perform differential gene expression, and generate volcano, violin and gene expression plots etc.
Once complete click 'GENERATE PLOT VIEWER'.
The data can now be saved (and loaded) as a VGAS Plot View file (.VGASpv) by selecting 'File -> Save as Plot View'.

OPTION 2: Loading from the VGAS Plot View file (.VGASpv)
Double-click the 'RNA-Seq Plot Viewer' option in the right panel without selecting any files in the left panel, then select the file.

UMAP, TSNE, Flow or any other X,Y coordinate data can be loaded in (after SKIP PLOT) by selecting 'File -> Load XYs'.

Plots (Plot View Data .VGASpvd) can be saved and loaded for any matching Plot View.

Plot Viewer Tutorial Videos

• Loading Data and Generating UMAPs

• Setting Default Colour Palettes

• Setting Default Gene Markers

• Genes: Sorting, Searching and Selecting.

• Metadata: Sorting, Searching and Selecting.

• Creating Groups

• Performing Differential Gene Expression

• Generating Volcano Plots

• Generating Gene Plots (Violin & Box plots etc.)

  • Colouring Gene Plot (Jitter) Points

  • Colouring Gene Plot (Jitter) Points using Heatmaps

• Selecting and Moving Plots

• Scaling Plot Axes

• Setting Point, Background, Highlights & Line Options.

• Highlighting and Hiding Plot Points

• Colouring Plots by Metadata

• Colouring Plots using Heatmaps

• Setting Plot Titles

• Setting Plot Labels/Legends

• Setting Heatmap Legends

• Resizing Text and Setting Fonts

• Setting Tool-tips

• Displaying Number of Cells with Expression Per Gene

• Displaying a Single Cells Expression Per Gene

• Displaying Number of Genes Expressed Per Cell

• Generating Gene Expression Level Plots

• Setting the Draw Order of the Plot Points

• Adding and Displaying Notes

• Exporting Plots as High Resolution Publication Ready Images

• Saving & Loading the Plot View Data