Table 1.
Resources for users about bigPint interactive graphics.
Table 2.
Examples of independent layers of interactivity.
Fig 1.
Step 1: Independent interactive layers of scatterplot matrix.
First step in a four-part example series of user actions. User hovers over background hexagon to determine it contains two genes.
Fig 2.
Step 2: Independent interactive layers of scatterplot matrix.
Second step in a four-part example series of user actions. User clicks on background hexagon to overlay the two corresponding genes as orange points in the foreground layer of each scatterplot. The computationally-expensive background layer of hexagons does not need to be redrawn.
Fig 3.
Step 3: Independent interactive layers of scatterplot matrix.
Third step in a four-part example series of user actions. The background layer of hexagons remains interactive and the user can still hover over another hexagon of interest to determine it contains 40 genes.
Fig 4.
Step 4: Independent interactive layers of scatterplot matrix.
Fourth step in a four-part example series of user actions. User clicks on background hexagon to overlay the 40 corresponding genes as orange points in the foreground layer of each scatterplot. This step does not require the computationally-expensive background layer of hexagons to be redrawn.
Fig 5.
Step 1: Independent interactive layers of litre plot.
First step in a four-part example series of user actions. User uses Shiny buttons to specify treatment pairs (N and P) and hexagon size (10) for drawing background hexagon layer. User can hover over hexagon of interest to determine it contains 19 genes.
Fig 6.
Step 2: Independent interactive layers of litre plot.
Second step in a four-part example series of user actions. User uses Shiny buttons to specify metric (FDR) and metric order (Increasing) to establish the order in which genes will be overlaid as pink points in the foreground layer. User clicks “Plot gene” button and the gene with the lowest FDR value (Glyma.19G168700.Wm82.a2.v1) is overlaid. The background layer of hexagons does not need to be redrawn.
Fig 7.
Step 3: Independent interactive layers of litre plot.
Third step in a four-part example series of user actions. User clicks “Plot gene” button again and the gene with the second-lowest FDR value (Glyma.13G293500.Wm82.a2.v1) is overlaid. This step does not require the background layer of hexagons to be redrawn.
Fig 8.
Step 4: Independent interactive layers of litre plot.
Fourth step in a four-part example series of user actions. User can zoom and pan on the layers using the Plotly Modebar.
Fig 9.
Step 1: Independent interactive layers of volcano plot.
First step in a four-part example series of user actions. User uses Shiny buttons to specify treatment pairs (N and P) and hexagon size (9) for drawing background hexagon layer. User can hover over hexagon of interest to determine it contains 1 gene.
Fig 10.
Step 2: Independent interactive layers of volcano plot.
Second step in a four-part example series of user actions. User uses Shiny buttons to specify log fold change and p-value thresholds. User clicks “Plot gene subset” button and the subset of genes that pass the thresholds are overlaid in the foreground layer as pink points. The background layer of hexagons does not need to be redrawn. User hovers over foreground point to view gene name (Glyma.19G168700.Wm82.a2.v1).
Fig 11.
Step 3: Independent interactive layers of volcano plot.
Third step in a four-part example series of user actions. User uses Shiny buttons to increase point size from 2 to 3. Foreground layer of pink points are increased in size and the background layer of hexagons does not need to be redrawn.
Fig 12.
Step 4: Independent interactive layers of volcano plot.
Fourth step in a four-part example series of user actions. User uses Shiny buttons to update threshold values and again presses “Plot gene subset” button. The subset of genes that pass the new thresholds are overlaid in the foreground layer as pink points. The background layer of hexagons does not need to be redrawn.
Fig 13.
Step 1: Consecutive box selection in parallel coordinate plot.
First step in a four-part example series of user actions. User selects the Box Select tool from the Plotly Modebar.
Fig 14.
Step 2: Consecutive box selection in parallel coordinate plot.
Second step in a four-part example series of user actions. User specifies box selection by drawing a rectangular query. Only the genes (pink lines) inside the specified rectangle remain.
Fig 15.
Step 3: Consecutive box selection in parallel coordinate plot.
Third step in a four-part example series of user actions. User can hover over a gene of interest (pink line) to view its name (Glyma.11G216300.Wm82.a2.v1).
Fig 16.
Step 4: Consecutive box selection in parallel coordinate plot.
Fourth step in a four-part example series of user actions. User can zoom and pan on the plot using the Plotly Modebar.