From 482bd140be38ff5524f59e5b1c353d0c7a3dd700 Mon Sep 17 00:00:00 2001 From: Philip Bulsink Date: Mon, 18 Nov 2024 08:51:21 -0500 Subject: [PATCH] Additional reference, minor changes. --- paper/paper.bib | 14 ++++++++++++++ paper/paper.md | 46 +++++++++++++++++++++++++--------------------- 2 files changed, 39 insertions(+), 21 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 0838b8c..25e8c11 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -25,3 +25,17 @@ @book{wickham:2016 url = {https://ggplot2.tidyverse.org}, doi = {10.32614/CRAN.package.ggplot2} } + +@article{rougier:2014, + author = {Rougier, Nicolas P. and Droettboom, Michael and Bourne, Philip E.}, + doi = {10.1371/journal.pcbi.1003833}, + issn = {1553-7358}, + journal = {PLoS Computational Biology}, + month = {sep}, + number = {9}, + pages = {e1003833}, + title = {{Ten Simple Rules for Better Figures}}, + url = {https://dx.plos.org/10.1371/journal.pcbi.1003833}, + volume = {10}, + year = {2014} +} diff --git a/paper/paper.md b/paper/paper.md index e3fb346..6c0f44e 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -3,7 +3,7 @@ title: 'PlotFTIR: Plotting FTIR Spectra' tags: - R - spectroscopy - - visualisation + - visualization - chemometrics authors: - name: Philip Bulsink @@ -35,26 +35,26 @@ manipulation capabilities. # Statement of need -`PlotFTIR` is a package that takes input data and produces high-quality, journal-article ready graphics, *reproducibly* -(\autoref{fig:example}). Scientists and researchers often rely on manual processes in software (such as Excel) to produce -graphics for journals, but these can be cumbersome and slow, requiring manual changes as new data is produced, or difficult -manipulations if the researcher needs to perform even simple manipulations (such as shifting spectra or averaging results). +`PlotFTIR` is a package that takes input data and produces high-quality, journal-article ready graphics, *reproducibly* and +with high-quality defaults (\autoref{fig:example}). Scientists and researchers often rely on manual processes in software +(such as Excel) to produce graphics for journals, but these can be cumbersome and slow, requiring manual changes as new data +is produced, or difficult changes if the researcher needs to perform even simple data manipulation (such as shifting spectra +or averaging results). Key components of producing high-quality figures are outlined by Rougier et. al. [@rougier:2014] and +the core principle of `PlotFTIR` is to follow these 'simple rules'. ![Example FTIR spectra produced by `PlotFTIR`.\label{fig:example}](./paper-biodiesel.png) -`PlotFTIR` is designed with a repeatable, object-oriented workflow in mind, enabling reproducible workflows from loading -data through saving graphical files. Users can easily run a short script on their data set to produce graphics, or use -a few functions to visualize important elements during exploratory data analysis. +`PlotFTIR` is designed with a repeatable, data- and plot-oriented workflow in mind, enabling reproducible workflows from +loading data through saving graphical files. Users can easily run a short script on their data set to produce graphics, +or use a few functions to visualize important elements during exploratory data analysis. `PlotFTIR` provides simple manipulation functions, such as averaging of spectra, addition/subtraction of scalar values, -multiple linear baselining functions, and conversion between absorbance and transmittance units (both commonly used in -FTIR studies, but each preferred by different scientific applications). - -More advanced spectra manipulation or chemometrics may be performed by other packages such as `ir` [@teickner:2022] or -`ChemoSpec` [@hanson:2024]. To facilitate collaboration between packages, `PlotFTIR` contains functions which can convert -data to or from the format specified by these other packages. This permits complex baseline, smoothing, or derivative -calculations in `ir`, or detailed statistics such as PCA, clustering, or ANOVA in `ChemoSpec`, and pretty plotting in -`PlotFTIR`, all in one workflow. +multiple (linear) baselining functions, and conversion between absorbance and transmittance units (both commonly used in +FTIR studies, but each preferred by different scientific applications). More advanced spectra manipulation or chemometrics +may be performed by other packages such as `ir` [@teickner:2022] or `ChemoSpec` [@hanson:2024]. To facilitate collaboration +between packages, `PlotFTIR` contains functions which can convert data to or from the format specified by these other +packages. This permits complex baseline, smoothing, or derivative calculations in `ir`, or detailed statistics such as PCA, +clustering, or ANOVA in `ChemoSpec`, and finishing with pretty plotting in `PlotFTIR`, all in one workflow. `PlotFTIR` supports annotation of graphics with markers and labels, simple title and legend changes, sample renaming functions, and output options. It also provides logical default graphical parameters, including titles, legends, @@ -63,12 +63,16 @@ the other `R` packages for FTIR which focus on spectra statistics or processing of publishing journal articles or reports (i.e. producing plots with normal x-axis orientation, default ggplot2 colour palettes and labels, no support for annotation beyond ggplot functions, etc.) [@teickner:2022; @hanson:2024]. -Since `PlotFTIR` produces graphics using `ggplot2`, it enables novice users to produce graphics easily without preventing -advanced users from performing customization using ggplot2 or other add-on packages [@wickham:2016]. Graphical functions -in `PlotFTIR` are designed to be used in a traditional step-wise or piped fashion, where multiple graphical manipulations -can be performed sequentially. +While `PlotFTIR` produces graphics using `ggplot2` [@wickham:2016], it enables novice users to produce graphics easily +without preventing advanced users from performing customization. Users need not know `ggplot2` functions to produce +`PlotFTIR` graphics, instead, the graphical functions in `PlotFTIR` are designed to be used in a traditional step-wise +or piped fashion where multiple graphical manipulations can be performed sequentially. However, should users more +comfortable with `R` and `ggplot2` feel the need, the entire plot can be modified to their purposes with `ggplot2` +manipulations. + +The documentation for `PlotFTIR` is available in English and French (including having default French labels and titles +available for plotting by setting `lang = 'fr'` in the initial arguments for the plot). -The documentation for `PlotFTIR` is available in English and French. # Acknowledgements