diff --git a/docs/images/sankey_preview.png b/docs/images/sankey_preview.png new file mode 100644 index 0000000..746f112 Binary files /dev/null and b/docs/images/sankey_preview.png differ diff --git a/docs/images/unity_3d_placeholder.png b/docs/images/unity_3d_placeholder.png index 1107b87..7f9930f 100644 Binary files a/docs/images/unity_3d_placeholder.png and b/docs/images/unity_3d_placeholder.png differ diff --git a/docs/readme.md b/docs/readme.md index 031aef6..39eaeb3 100644 --- a/docs/readme.md +++ b/docs/readme.md @@ -1,6 +1,6 @@ # **Companion Website for "Constructing and Using Cell Type Populations for the Human Reference Atlas"** -Andreas Bueckle1,4,\*\*, Bruce William Herr II1, Lu Chen2, Daniel Bolin1, Vicky Daiya1, Devin Wright1, Dan Qaurooni1, Kristin Ardlie3, Fusheng Wang2, Katy Börner1,\* +Andreas Bueckle1,4,\*\*, Bruce William Herr II1, Lu Chen2, Daniel Bolin1, Danial Qaurooni1, Michael Ginda1, , Kristin Ardlie3, Fusheng Wang2, Katy Börner1,\* 1 Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA \ 2 Department of Computer Science and Department of Biomedical Informatics, Stony Brook University, Stony Brook, 11794, NY, USA \ @@ -44,15 +44,12 @@ Code to demonstrate how 3D cells can be generated with Python is available [here alt_text +# Interactive Sankey Diagram +Atlas-level data for HRApop v0.10.0 comes from various sources and . The Sankey diagram below offers an overview of the distribution of HRApop datasets along demographic, informatical, and biomedical markers. -# Bar graphs for cell type populations - -Shown here are bar graphs for the cell type populations of the four anatomical structures shown in the kidney above (VH female, left) specifically for the cortex and three renal pyramids, based on collision detection results from eight tissue blocks. Visualized are 331,010 cells of 50 unique types. Note that the y-axis is scaled logarithmically to account for the vast ranges in numbers of cells per cell types. - -**This will be replaced with updated bar graphs.** - -alt_text +load_button +alt_text # Single-cell proteomics data diff --git a/plots_paper/PlotsPaper.R b/plots_paper/PlotsPaper.R index 11581b8..6126f30 100644 --- a/plots_paper/PlotsPaper.R +++ b/plots_paper/PlotsPaper.R @@ -262,7 +262,7 @@ p <- sankeyNetwork(Links = prep_links, Nodes = nodes, Source = "source", p -sankeyPlot$save('mychart.html', standalone = TRUE) +saveNetwork(p, "../docs/sankey.html") # Fig. SankeyScatter scatter graph scatter = read_csv(paste("../../hra-pop/output-data/v",hra_pop_version,"/reports/atlas/validation-v5.csv", sep=""))