fix links and figs

index.md

@@ -11,9 +11,9 @@ What is `bngal`?
 
 Biological Network Graph Analysis and Learning (`bngal`) is a package written in R to create high-quality, complex correlation networks from microbial abundance data.
 
-<object data="../figures/all-asv-by-edge_btwn_cluster.pdf" type="application/pdf" width="700px" height="700px">
-    <embed src="../figures/all-asv-by-edge_btwn_cluster.pdf">
-        <p>This browser does not support PDFs. Please download the PDF to view it: <a href="../figures/all-asv-by-edge_btwn_cluster.pdf">Download PDF</a>.</p>
+<object data="./figures/all-asv-by-edge_btwn_cluster.pdf" type="application/pdf" width="700px" height="700px">
+    <embed src="./figures/all-asv-by-edge_btwn_cluster.pdf">
+        <p>This browser does not support PDFs. Please download the PDF to view it: <a href="./figures/all-asv-by-edge_btwn_cluster.pdf">Download PDF</a>.</p>
     </embed>
 </object>
 

quick-start.markdown

@@ -8,7 +8,7 @@ permalink: /quick-start-global-net/
 
 # Global network analysis
 
-Creating a "global network" means you are sending all of your taxonomic abundance data into the `bngal` pipeline. This is a useful starting analysis that visualizes broad trends across your entire dataset. The following global network example will analyze a [published dataset](https://journals.asm.org/doi/10.1128/aem.01682-23#supplementary-materials) to show the potential for regional biogeography of microbes living in the eastern Yucatan carbonate aquifer. After such a global analysis, we can [split up the data into separate networks](#separate-networks-by-metadata-column-region) based on a metadata column (`region`) to further refine pairwise correlation trends within each region.
+Creating a "global network" means you are sending all of your taxonomic abundance data into the `bngal` pipeline. This is a useful starting analysis that visualizes broad trends across your entire dataset. The following global network example will analyze a [published dataset](https://journals.asm.org/doi/10.1128/aem.01682-23#supplementary-materials) to show the potential for regional biogeography of microbes living in the eastern Yucatan carbonate aquifer. After such a global analysis, we can [split up the data into separate networks](../quick-start-multi-net) based on a metadata column (`region`) to further refine pairwise correlation trends within each region.
 
 ## Step 1: `bngal-build-nets`