diff --git a/paper/paper.md b/paper/paper.md index b5b6aec..6ac6823 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -18,10 +18,6 @@ authors: - name: Author with no affiliation corresponding: true # (This is how to denote the corresponding author) affiliation: 3 - - given-names: Ludwig - dropping-particle: van - surname: Beethoven - affiliation: 3 affiliations: - name: University of Wisconsin-Madison, USA index: 1 @@ -60,13 +56,13 @@ In applying the dashboard, we made an extended time series by connecting the las # Usage -The source code for `MolPad` is stored on [Github](https://github.com/KaiyanM/MolPad). The app is hosted in the eponymous R package which can be downloaded and run on a local computer. We anticipate that some users may need more flexibility in their analyses, requiring backend R coding for tasks like setting up detailed operating models or download figure outputs. For such needs, the essential set of R functions employed in the Shiny app is accessible through the R package. +The source code for `MolPad` is stored on [Github](https://github.com/KaiyanM/MolPad). The app is hosted in the eponymous R package which can be downloaded and run on a local computer. We anticipate that some users may need more flexibility in their analyses, requiring backend R coding for tasks like setting up detailed operating models or downloading figure outputs. For such needs, the essential set of R functions employed in the Shiny app is accessible through the R package. # Figures ![Dashboard Overview: `A`: cluster-level network, `B`: taxonomic-level bar plot, `C`: a type-level line plot, and `D`: a feature-level table. \label{fig:dashboard}](dashboard.png) -![Example of discoversing related patterns with network plot. For `a`, the two linked nodes are in the dashed box and have a closer inverse pattern than the other. For `b`, these groups are both less volatile on average and have similar inverse patterns.\label{fig:pattern}](pattern.png){ width=50% } +![Example of discovering related patterns with network plot. For `a`, the two linked nodes are in the dashed box and have a closer inverse pattern than the other. For `b`, these groups are both less volatile on average and have similar inverse patterns.\label{fig:pattern}](pattern.png){ width=50% } ![Dashboard showing Groups 10, 7, 4, and 3 for the bacterial(a.) and Group 4 for the eukaryotic(b.) community. Groups 10 and 4 have decreasing trends for both cheeses, and they all include largely Proteobacteria and Firmicutes. While Groups 3 and 7 have the opposite increasing trends, which include more Actinobacteria and Bacteroidetes. Among these, Groups 7 and 4 have the strongest periodicity, suggesting a more reproducible tendency for the corresponding main components. For the eukaryote community, most of the features followed the same stable pattern as in Group 4\label{fig:cheesecase}](cheesecase.png){ width=80% }