VGAS RNAseq :: Options for Heatmap Colouring скачать в хорошем качестве

VGAS RNAseq :: Options for Heatmap Colouring

This tutorial demonstrates how to use the Visual Genomics Analysis Studio (VGAS) to colour plots using heatmap colouring. There are multiple ways to apply heatmap colours to a plot. FIRST OPTION (1) Select the plot to apply heatmap colouring to, and then select the gene that will be presented. (2) Click the button with the multiple lines at the bottom right of the genes panel to heat-map cells in the order shown in the sample/cell metadata grid. (3) Click the line button at the bottom right of the genes panel to plot cells in the default order (being the order that cells were loaded into VGAS) (4) The Up and Down arrows change the draw order for increasing and decreasing expression to more clearly show the heatmap colouring. SECOND OPTION (1) Another way for a user to heatmap a specific gene is by setting the gene as metadata (either in the metadata panels or the sample/cell metadata grid) (2) Right-click on the metadata panel and select "Update Coverage Depth Bar" to update the scale according to distribution of gene expression. (3) Select “Set heatmap colour range” to alter the scale based on the distribution of expression (4) To set heatmap colours in accordance with heatmap scale (inclusive of depth bar and range), choose “Set Heatmap Colours” and then “by Scale”. (Setting by grid will not incorporate the coverage depth or the colour range) (5) The depth bar and scale can be viewed alongside the plot by ticking show heatmap scale and depth bar. To move the scales select "Move". (6) To update plots in real-time, tick the “Update Plots” box in the “Colour Options” panel, and slide the scale above the coloured bar to adjust heatmap colouring scale. (7) To change the colour of the scale to one of the preset heatmap colourings in the grid, select the desired one and then set scale. (8) Heatmap scale colours can also be selected manually, by clicking on any of the five coloured boxes and then selecting desired colours. (9) A range can also be set for metadata expression (10) Users can also opt to set a minimum value and colour to their heatmaps. This will plot everything below this value in the selected colour. (11) The option circles allow user to toggle between metadata panels. The first to circles represent the two metadata panels, and the other four circles represent the four metadata columns in the grid. Visit https://www.iiid.com.au/software/vgas for more tutorials on how to use VGAS. To request a trial version of VGAS, contact: [email protected]