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KaiyanM authored Nov 18, 2023
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- 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
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# 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% }
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