From 50314578abeee541aa90b7aa4b37f70bc90699b0 Mon Sep 17 00:00:00 2001 From: KaiyanM Date: Sat, 18 Nov 2023 16:52:30 -0600 Subject: [PATCH 1/3] Update DESCRIPTION --- DESCRIPTION | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cd01964..e8bdbf3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,10 +3,9 @@ Title: MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitud Version: 1.0.0 Authors@R: person("Kaiyan", "Ma", , "kaiiyenma@gmail.com", role = c("aut", "cre"), - comment = c(ORCID = "YOUR-ORCID-ID")) + comment = c(ORCID = "0000-0002-7355-8924")) Description: MolPad offers a visualization dashboard tool designed to enhance our understanding of how molecular co-expression works in the context of multi-omics microbiome data. The approach involves using a cluster network to provide an initial overview of relationships across multiple omics, with the added functionality to interactively zoom in on specific areas of interest. To facilitate this analysis, we've developed a focus-plus-context strategy that seamlessly connects to online curated annotations. -License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a - license +License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a license Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 From 12281584633752b16f97f2c0845681e3bc7f0330 Mon Sep 17 00:00:00 2001 From: KaiyanM Date: Sat, 18 Nov 2023 16:54:32 -0600 Subject: [PATCH 2/3] Update paper.md --- paper/paper.md | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) 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% } From 8417a4b20d9591602031ed0a8c6d305bec445b6d Mon Sep 17 00:00:00 2001 From: KaiyanM Date: Sat, 18 Nov 2023 16:56:48 -0600 Subject: [PATCH 3/3] Update paper.md --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 6ac6823..5bd9e69 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -62,7 +62,7 @@ The source code for `MolPad` is stored on [Github](https://github.com/KaiyanM/Mo ![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 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% } +![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=60% } ![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% }