Merge pull request #24 from cns-iu/update-copmpanion-website

Added language re: heatmaps

docs/readme.md

@@ -72,7 +72,7 @@ The Linked Open Data (LOD) server supports [SPARQL](https://sparql.dev/) querie
 <a target="_blank" href="images/SI-fig2b-hrapop-heatmap_celltypist.png"><img alt="alt_text" width="75%" src="images/SI-fig2b-hrapop-heatmap_celltypist-cte.png"></a>
 <a target="_blank" href="images/SI-fig2c-hrapop-heatmap_popv.png"><img alt="alt_text" width="75%" src="images/SI-fig2c-hrapop-heatmap_popv-cte.png"></a>
 
-**SI Figure 2. Heatmaps for prevalence of cell type across organs in HRApop dataset. a.** Azimuth can be run over 4 organs. **b.** CellTypist is available for six organs. **c.** popV was run for 10 organs. Each heatmap box represents a scaled mean value (z-score) for percentage of cells identified in each data set. A score of 3 indicates that the value is 3 standard deviations from the mean of a given cell type across data sets for a given tool. Full versions for all three plots are provided [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_azimuth.png) (Azimuth), [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_celltypist.png) (CellTypist), and [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_popv.png) (popV). The R Markdown document to generate these visualizations is [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/HRA_HeatmapAnalysis_CellTypePer.Rmd). 
+**SI Figure 2. Heatmaps for prevalence of cell type across organs in HRApop dataset. a.** Azimuth can be run over 4 organs. **b.** CellTypist is available for six organs. **c.** popV was run for 10 organs. Each heatmap box represents a scaled mean value (z-score) for percentage of cells identified in each data set. A score of 3 indicates that the value is 3 standard deviations from the mean of a given cell type across data sets for a given tool. The heatmap uses a scaled average percentage of cell types found across datasets for the same organ. The percentage values are scaled using R's [scale()](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/scale) function, where values for a given variable are centered around the mean, and the scaled to the standard deviation from the mean, aka given a z-score. A z-score of 0 means these values are close to the variable's mean value, which, in our case, are cell type values of 0. A color corresponding to a score of 1 would indicate that the cell type percentage values is 1 standard deviation from the mean for that cell type, values of 3 would be 3 standard deviations from the mean, etc. Full versions for all three plots are provided [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_azimuth.png) (Azimuth), [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_celltypist.png) (CellTypist), and [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/hrapop-heatmap_popv.png) (popV). The R Markdown document to generate these visualizations is [here](https://github.com/cns-iu/hra-construction-usage-supporting-information/blob/main/analysis_and_plots/HRA_HeatmapAnalysis_CellTypePer.Rmd). 
 
 <a target="_blank" href="images/SI-Fig3.png"><img alt="alt_text" width="75%" src="images/SI-Fig3-cte.png"></a>