Infovis Charts Extensions
Minerva allows adding interactive charts to story points. These visualizations give the viewer additional data statistics. In the current version, the user can choose between bar charts, matrices, and scatterplots. The charts can be linked to the image space. User interactions within the chart can trigger overlays, panning and zooming, as well as pointing to specific cells and regions in the image browser.
The scatterplot chart allows showing any two metric dimensions up to a few thousand data points. Users can define colors, labels, and axes descriptions, as well as an introductory text. The screenshot below shows a U-Map projection where colors and labels are set according to cell phenotypes. Hovering over the data points reveals additional information that can be specified. Clicking on a data point can trigger a zooming/panning event and an arrow glyph to show the cell's position in the image.
Chart creation is not yet part of the authoring tool but authors can easily add a chart to the yaml file that contains the story descriptions.
- Name: UMAP
Group: Structural Components
Audio: /assets/audio/speech_20190918201156545.mp3
VisScatterplot:
data: /assets/visdata/LUNG_3_UMAP_data_20200218.csv
clusters:
labels: Tumor,Other,Immune,Stromal
colors: e41a1c, 377eb8, 4daf4a, 984ea3
reorder: Tumor,Stromal,Immune,Other
axes:
x: UMAP_D1
y: UMAP_D2
Description: Description here</code>
displays the data:
"","Cell_ID","clust_ID","X_position","Y_position","UMAP_D1","UMAP_D2"
"1",57804,3,14242.6545454546,4537.25454545455,2.20106819588499,2.97097283790507
"2",45008,2,12242.1417910448,5073.0223880597,1.82707837009708,0.713481790466293
"3",80565,4,7418.20614035088,8242.4649122807,-2.86151483486962,-1.49183606602466
where UMAP_D1 and UMAP_D2 are set as axes and X_position and Y_position to link to the cell position in image space.
The matrix chart allows to plot aggregated channel information and groups such as phenotype clusters against each other and to visualize correlations. Charts adapt automatically to the number of rows and columns in the dataset. Click events on a matrix column, e.g., CD45, can trigger to show a respective image overlay.
Chart creation is not yet part of the authoring tool but authors can easily add a chart to the yaml file that contains the story descriptions.
- Name: K-means Clustering
Group: Structural Components
Audio: /assets/audio/speech_20190918201156545.mp3
VisMatrix: /assets/visdata/clust4hpdat_LUNG-3-PR.csv
displays (left matrix in image) the data:
ClustName,KERATIN,ASMA,CD45
Tumor,0.356225098,-0.454998929,-0.085779064
Stromal,-0.345658946,0.213412916,-0.206773617
Immune,-0.304689947,-0.119950697,0.445621169
Other,-0.296644655,-0.317059176,-0.043042572
