From d3f885c3908dc9a180b89de8b2311311c6ddd704 Mon Sep 17 00:00:00 2001 From: Roni Choudhury Date: Fri, 9 Oct 2020 12:46:46 -0400 Subject: [PATCH 1/3] Expand KNN acronym --- joss/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/joss/paper.md b/joss/paper.md index 92150be87..fa64104e7 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -118,7 +118,7 @@ missing completely at random (MCAR) or missing not at random (MNAR). For each type, an imputation mode is automatically performed but the options may be adjusted to apply different algorithms, including random -forest, KNN, mean, or median imputation modes for completely at random +forest, K neareset neighbors, mean, or median imputation modes for completely at random missingness (MCAR) and zero or half-minimum imputation for not-at-random missingness (MNAR). From ae24ac7b69933c5300f42ff2c225623036cc1ca7 Mon Sep 17 00:00:00 2001 From: Roni Choudhury Date: Fri, 9 Oct 2020 12:46:58 -0400 Subject: [PATCH 2/3] Fix typo --- joss/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/joss/paper.md b/joss/paper.md index fa64104e7..f90091c79 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -377,7 +377,7 @@ Among the most well-known metabolomics workflow tools are MetaboAnalyst which include MS spectral processing and have statistical analyses and visualization tools that are generally similar to Viime. -An exhaustive feature comparison of with these other platforms is beyond the +An exhaustive feature comparison with these other platforms is beyond the scope of this paper, but a major distinguishing feature of Viime is its emphasis on ease of use and interactivity. Only XCMS and MetaboAnalyst are simple, readily accessible web applications that require no existing package (e.g. R), From f3169e6cb649e22e54f7e4084edf45472ece1173 Mon Sep 17 00:00:00 2001 From: Roni Choudhury Date: Fri, 9 Oct 2020 12:47:28 -0400 Subject: [PATCH 3/3] Reflow text --- joss/paper.md | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/joss/paper.md b/joss/paper.md index f90091c79..5c2447851 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -112,15 +112,13 @@ analysis. ## Data Imputation -Once errors are corrected, data imputation is automatically performed. -For metabolites with missing values, the type of missingness is classified as +Once errors are corrected, data imputation is automatically performed. For +metabolites with missing values, the type of missingness is classified as missing completely at random (MCAR) or missing not at random (MNAR). For each type, an imputation mode is automatically performed but the options may be -adjusted to apply different algorithms, including -random -forest, K neareset neighbors, mean, or median imputation modes for completely at random -missingness (MCAR) and zero or half-minimum imputation for not-at-random -missingness (MNAR). +adjusted to apply different algorithms, including random forest, K neareset +neighbors, mean, or median imputation modes for completely at random missingness +(MCAR) and zero or half-minimum imputation for not-at-random missingness (MNAR). ![Dynamically updating customizable plots which animate to show immediate feedback when adjusting pretreatment options.](figures/figure3.png) @@ -377,12 +375,12 @@ Among the most well-known metabolomics workflow tools are MetaboAnalyst which include MS spectral processing and have statistical analyses and visualization tools that are generally similar to Viime. -An exhaustive feature comparison with these other platforms is beyond the -scope of this paper, but a major distinguishing feature of Viime is its emphasis -on ease of use and interactivity. Only XCMS and MetaboAnalyst are simple, -readily accessible web applications that require no existing package (e.g. R), -downloads or connection to the Galaxy platform. The unique user interactivity in -Viime starts with the ability to simply drag and drop CSV or Excel files and +An exhaustive feature comparison with these other platforms is beyond the scope +of this paper, but a major distinguishing feature of Viime is its emphasis on +ease of use and interactivity. Only XCMS and MetaboAnalyst are simple, readily +accessible web applications that require no existing package (e.g. R), downloads +or connection to the Galaxy platform. The unique user interactivity in Viime +starts with the ability to simply drag and drop CSV or Excel files and interactively assign the sample identifiers, comparison groups, metadata, and metabolites. Dynamic visualization of the PCA scores and loadings plots with different types of data (e.g. NMR, LC-MS, and GC-MS) and data treatments (e.g.