diff --git a/DESCRIPTION b/DESCRIPTION index 4aa4956..4bb420d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FREDA Title: An app for the processing and visualization of Fourier-transform mass spectrometry data. -Version: 1.2.4 +Version: 1.3.0 Authors@R: c(person("Lisa", "Bramer", "lisa.bramer@pnnl.gov", role = "aut", "cre"), person("Daniel", "Claborne", "daniel.claborne@pnnl.gov", role = c("aut"))) Description: A frontend application which exposes functionality of the ftmsRanalysis R package. See @@ -22,8 +22,7 @@ Imports: markdown, pander, plotly, - purrr, - raster, + purrr, RColorBrewer, readr, reshape2, @@ -47,6 +46,5 @@ Imports: xfun, MetaCycData, mapDataAccess, - ftmsRanalysis, - datadr + ftmsRanalysis diff --git a/Reactive_Variables/visualize_revals.R b/Reactive_Variables/visualize_revals.R index 39150d1..9d2e7fe 100644 --- a/Reactive_Variables/visualize_revals.R +++ b/Reactive_Variables/visualize_revals.R @@ -149,7 +149,7 @@ plot_data <- eventReactive(input$plot_submit, { validate(need(input$summary_fxn %in% ftmsRanalysis:::getGroupComparisonSummaryFunctionNames(), "Please select a summary function")) # get the value of the single pairwise comparison - grpComparisonsObj <- divideByGroupComparisons(temp_data, comparisons = "all")[[1]]$value + grpComparisonsObj <- divideByGroupComparisons(temp_data, comparisons = "all")[[1]] # paramaters specific to uniqueness_gtest() if (input$summary_fxn == "uniqueness_gtest") { diff --git a/calculation_options.csv b/calculation_options.csv index d81d762..fa11a42 100644 --- a/calculation_options.csv +++ b/calculation_options.csv @@ -1,7 +1,7 @@ "DisplayName","Function","Info" "Element Ratios","calc_element_ratios","Element ratios for each molecule" "Kendrick Mass and Defect","calc_kendrick","Kendrick Defect = Nominal Kendrick Mass - Kendrick Mass \n\n Kendrick MAss = IUPAC mass*(14/14.01565), where IUPAC mass is based on the 12C atomic mass as exactly 12 Da. [Hughey et al., 2001]" -"NOSC","calc_nosc","Nominal oxidation state of carbon. [Koch \& Dittmar, 2006][Erratum]" +"NOSC","calc_nosc","Nominal oxidation state of carbon. [LaRowe & Van Cappellen, 2011]" "Gibbs Free Energy","calc_gibbs","Cox Gibbs Free Energy. Calculated as:60.3 - 28.5*NOSC [LaRowe & Van Cappellen, 2011]" "Aromaticity & Modified Aromaticity","calc_aroma","Aromaticity & Modified Aromaticity. [Koch \& Dittmar, 2006] [Erratum]" "DBE, DBE - O & DBE - AI","calc_dbe","DBE & DBE - O [Koch \& Dittmar, 2006] [Erratum]" diff --git a/global.R b/global.R index 3be99ab..c2550df 100644 --- a/global.R +++ b/global.R @@ -8,7 +8,6 @@ library(webshot) library(htmlwidgets) library(dplyr) library(markdown) -library(raster) library(purrr) library(shinyBS) library(shinyjs) diff --git a/renv.lock b/renv.lock index a6d54a4..71b73a5 100644 --- a/renv.lock +++ b/renv.lock @@ -281,16 +281,6 @@ ], "Hash": "5edbbabab6ce0bf7900a74fd4358628e" }, - "codetools": { - "Package": "codetools", - "Version": "0.2-19", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c089a619a7fae175d149d89164f8c7d8" - }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", @@ -368,28 +358,6 @@ ], "Hash": "38bbf05fc2503143db4c734a7e5cab66" }, - "datadr": { - "Package": "datadr", - "Version": "0.8.6", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteRepo": "datadr", - "RemoteUsername": "delta-rho", - "RemoteRef": "HEAD", - "RemoteSha": "f3ffebd8e1c43a5d11cd3543bbe672c88f8c52f3", - "Requirements": [ - "codetools", - "data.table", - "digest", - "dplyr", - "hexbin", - "magrittr", - "methods", - "parallel" - ], - "Hash": "4ddf60dd3cd5d3baf559f44d872fc74e" - }, "digest": { "Package": "digest", "Version": "0.6.37", @@ -487,13 +455,13 @@ "Package": "ftmsRanalysis", "Version": "1.1.0", "Source": "GitHub", - "Remotes": "github::delta-rho/datadr, github::EMSL-Computing/MetaCycData", + "Remotes": "github::EMSL-Computing/MetaCycData", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteRepo": "ftmsRanalysis", - "RemoteUsername": "EMSL-Computing", - "RemoteRef": "8753cb08900045e0763e9be7aa293e98de62a490", - "RemoteSha": "8753cb08900045e0763e9be7aa293e98de62a490", + "RemoteUsername": "EMSL-computing", + "RemoteRef": "8590e0dea16084238c82364706db9855c00801de", + "RemoteSha": "8590e0dea16084238c82364706db9855c00801de", "Requirements": [ "R", "RColorBrewer", @@ -514,7 +482,7 @@ "tidyr", "vegan" ], - "Hash": "0f4f9535c3cf1fcda1ad376ca0bcf0b4" + "Hash": "b973a46e6fe6ee30e4b8f03067dca5e2" }, "generics": { "Package": "generics", @@ -603,23 +571,6 @@ ], "Hash": "24b224366f9c2e7534d2344d10d59211" }, - "hexbin": { - "Package": "hexbin", - "Version": "1.28.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "lattice", - "methods", - "stats", - "utils" - ], - "Hash": "124e384c01d8746f1c12f9dc1b80a161" - }, "highr": { "Package": "highr", "Version": "0.11", @@ -1176,20 +1127,6 @@ ], "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, - "raster": { - "Package": "raster", - "Version": "3.6-26", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "methods", - "sp", - "terra" - ], - "Hash": "7d6eda494f34a644420ac1bfd2a8023a" - }, "readr": { "Package": "readr", "Version": "2.1.5", diff --git a/ui.R b/ui.R index 8ea87bd..4b07e30 100644 --- a/ui.R +++ b/ui.R @@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(), ), navbarPage( - title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.5")), + title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.3.0")), windowTitle = 'FREDA', id = "top_page", theme = "yeti.css", @@ -479,7 +479,7 @@ ui <- tagList(useShinyjs(), checkboxGroupInput("download_selection", label = "Check Download Selection", choices = c('Data File as one .csv and Molecular Identification File as another .csv' = "separate", 'Merged Data File and Molecular Identification File as a single .csv' = "merged", - 'Data summaries for grouped plots' = "group_data"), + 'Data summaries and comparison results for grouped plots' = "group_data"), width = "80%") ) ),