Merge pull request #11 from p2m2/develop

0.0.2
p2m2 · Mar 20, 2023 · d502c40 · d502c40
2 parents ad03970 + 1982f67
commit d502c40
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Showing 8 changed files with 131 additions and 110 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -22,13 +22,12 @@ workflows:
             - build
           context:
             - DOCKER_CONTEXT
+            - GITHUB_CONTEXT
             - SHINYAPP_CONTEXT
           filters:
             tags:
               only: /.*/
-            branches:
-              only:
-                - develop
+
 jobs:
   build:
     working_directory: ~/tmp
@@ -96,5 +95,7 @@ jobs:
       - run:
           name: deployment on https://www.shinyapps.io/
           command: |
-            [ -z "${CIRCLE_TAG}" ] && export APP_NAME="${CIRCLE_PROJECT_REPONAME}-${CIRCLE_BRANCH}" || export APP_NAME="${CIRCLE_PROJECT_REPONAME}"
+            # publish only tag release
+            export APP_NAME="${CIRCLE_PROJECT_REPONAME}"
+            export GITHUB_PAT=${GITHUB_TOKEN}
             ./publish_rshinyapp.sh
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: oligopeptidesMatching
 Title: Library of functions for in silico construction and detection of oligopeptides
 Description: In order to compute from amino acids molecular weight the putative oligomers of various oligomerization degree.
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person(given = "Kevin",
            family = "Billet",

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # oligopeptides_matching
 
 [![p2m2](https://circleci.com/gh/p2m2/oligopeptides_matching.svg?style=shield)](https://app.circleci.com/pipelines/github/p2m2)
-[![](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://p2m2.shinyapps.io/oligopeptides_matching/)
+[![](https://img.shields.io/badge/stable-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://p2m2.shinyapps.io/oligopeptides_matching/)
 
 In order to compute from amino acids molecular weight the putative oligomers of various oligomerization degree
 
@@ -109,12 +109,11 @@ install.packages("shiny")
 install.packages("DT")
 
 library(shiny)
-library(DT)
 
 library(devtools)
 library(roxygen2)
 document()
-runApp("exampleOligopeptidesMatching_aa")
+runApp("oligopeptides_matching")
 ```
 
 ### Examples

diff --git a/oligopeptides_matching/app.R b/oligopeptides_matching/app.R
@@ -1,99 +1,6 @@
 library(shiny)
-library(DT)
 
-# Constants
-### Amino acids
-aa <- c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y")
-
-### amino acids molecular weight
-mass_aa <- c(89.047679, 121.019751, 133.037509, 147.053159, 165.078979, 
-              75.032029, 155.069477, 131.094629, 146.105528, 131.094629,
-              149.051051,132.053493, 115.063329, 146.069143, 174.111676,
-              105.042594,119.058244, 117.078979,204.089878, 181.073894)
-
-aa_mw <- setNames(mass_aa, aa)
-
-### Polyphenols
-polyphenol <- c("Cyanidin",
-                "Cyanidin 3,5-O-diglucoside",
-                "Cyanidin 3-O-(6''-acetyl-galactoside)",
-                "Cyanidin 3-O-(6''-acetyl-glucoside)",
-                "Cyanidin 3-O-(6''-caffeoyl-glucoside)")
-
-### polyphenol molecular weight
-mass_polyphenol <- c(287.244, 611.525,491.422, 491.422, 611.527)
-
-pp_mw <- setNames(mass_polyphenol, polyphenol)
-
-### reaction elements
-H2O <- 18.010565
-H <- 1.007825
-
-ionization_list = stats::setNames(c(H),c("H"))
-
-
-# See above for the definitions of ui and server
-ui <- fluidPage(
-
-  # App title ----
-  titlePanel("Oligopeptides Matching"),
-
-  # Sidebar layout with a input and output definitions ----
-  sidebarLayout(
-
-    # Sidebar panel for inputs ----
-    sidebarPanel(
-
-    # Input: Numeric entry for number of obs to view ----
-    numericInput(inputId = "od",
-                   label = "Oligomerization degree:",
-                   value = 3),
-    numericInput(inputId = "mz_obs",
-                   label = "M/z observed :",
-                   value = 953.669),
-    numericInput(inputId = "ppm_error",
-                   label = "Tolerance:",
-                   value = 10)
-    ),
-    # Main panel for displaying outputs ----
-    mainPanel(
-        h3("Oligopeptides"),
-        # Output: HTML table with requested number of observations ----
-        DT::dataTableOutput("view")
-    )
-  )
-)
-
-server <- function(input, output) {
-
-
-
-  output$view <- DT::renderDataTable(
-    {aa_combined <- get_oligopeptides(
-      aminoacids = aa_mw,
-      chemical_reaction = H2O,
-      ionization = ionization_list,
-      oligomerization_degree = input$od)
-
-    aa_combined_names <- c(aa_combined$id)
-    aa_combined_mass <- c(aa_combined$MW)
-    aa_combined_mw <- setNames(aa_combined_mass, aa_combined_names)
-
-    combined_compounds <- get_combination_compounds(
-                              compounds_1 = aa_combined_mw,
-                              compounds_2 = pp_mw,
-                              chemical_reaction = H2O,
-                              ionization = setNames(c(H), c("H")))
-    mz_obs <- 953.669
-    combined_compounds_near_obs <-
-      match_mz_obs(input$mz_obs, combined_compounds,
-        ppm_error = input$ppm_error)
-
-    return(combined_compounds_near_obs)
-    }
-
-  )
-
-}
+source(server.R)
+source(ui.R)
 
 shinyApp(ui = ui, server = server)
diff --git a/oligopeptides_matching/data.R b/oligopeptides_matching/data.R
@@ -0,0 +1,29 @@
+# Constants
+### Amino acids
+aa <- c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y")
+
+### amino acids molecular weight
+mass_aa <- c(89.047679, 121.019751, 133.037509, 147.053159, 165.078979, 
+              75.032029, 155.069477, 131.094629, 146.105528, 131.094629,
+              149.051051,132.053493, 115.063329, 146.069143, 174.111676,
+              105.042594,119.058244, 117.078979,204.089878, 181.073894)
+
+aa_mw <- setNames(mass_aa, aa)
+
+### Polyphenols
+polyphenol <- c("Cyanidin",
+                "Cyanidin 3,5-O-diglucoside",
+                "Cyanidin 3-O-(6''-acetyl-galactoside)",
+                "Cyanidin 3-O-(6''-acetyl-glucoside)",
+                "Cyanidin 3-O-(6''-caffeoyl-glucoside)")
+
+### polyphenol molecular weight
+mass_polyphenol <- c(287.244, 611.525,491.422, 491.422, 611.527)
+
+pp_mw <- setNames(mass_polyphenol, polyphenol)
+
+### reaction elements
+H2O <- 18.010565
+H <- 1.007825
+
+ionization_list = stats::setNames(c(H),c("H"))
diff --git a/oligopeptides_matching/server.R b/oligopeptides_matching/server.R
@@ -0,0 +1,42 @@
+library(shiny)
+library(DT)
+library(oligopeptidesMatching)
+
+source("./data.R")
+
+server <- function(input, output) {
+
+  combination_compounds <- reactive({
+        aaa_combined <- get_oligopeptides(
+      aminoacids = aa_mw,
+      chemical_reaction = H2O,
+      ionization = ionization_list,
+      oligomerization_degree = input$od)
+
+    aa_combined <- as.data.frame(aaa_combined)
+    aa_combined_names <- c(aa_combined$id)
+    aa_combined_mass <- c(aa_combined$MW)
+    aa_combined_mw <- setNames(aa_combined_mass, aa_combined_names)
+
+    return(get_combination_compounds(compounds_1 = aa_combined_mw, 
+                              compounds_2 = pp_mw, 
+                              chemical_reaction = H2O, 
+                              ionization = setNames(c(H),c("H"))))
+  })
+  # =====
+  # All arrangement AA with PolyPhenols
+  output$view_arrangement <- DT::renderDataTable(
+    combination_compounds()
+  )
+  # =====
+  # Filtering on a single Value
+
+  output$view_filter_mz_obs <- DT::renderDataTable(
+     {
+      return(match_mz_obs(
+        input$mz_obs,
+        combination_compounds(),
+        ppm_error = input$ppm_error))
+    }
+  )
+}
diff --git a/oligopeptides_matching/ui.R b/oligopeptides_matching/ui.R
@@ -0,0 +1,44 @@
+ui <- navbarPage("Oligopeptides Matching",
+  tabPanel("Combination AA Polyphenol",
+
+  # Sidebar layout with a input and output definitions ----
+  sidebarLayout(
+
+    # Sidebar panel for inputs ----
+    sidebarPanel(
+    # Input: Numeric entry for number of obs to view ----
+    numericInput(inputId = "od",
+                   label = "Oligomerization degree:",
+                   value = 3)
+    ),
+    # Main panel for displaying outputs ----
+    mainPanel(
+        h3("Oligopeptides"),
+        # Output: HTML table with requested number of observations ----
+        DT::dataTableOutput("view_arrangement")
+    )
+  )
+),
+tabPanel("Match a single Mz",
+# Sidebar layout with a input and output definitions ----
+  sidebarLayout(
+
+    # Sidebar panel for inputs ----
+    sidebarPanel(
+    numericInput(inputId = "mz_obs",
+                   label = "M/z observed :",
+                   value = 953.669),
+    numericInput(inputId = "ppm_error",
+                   label = "Tolerance:",
+                   value = 10)
+    ),
+    # Main panel for displaying outputs ----
+    mainPanel(
+        h3("Oligopeptides"),
+        # Output: HTML table with requested number of observations ----
+        DT::dataTableOutput("view_filter_mz_obs")
+    )
+  )
+),
+tabPanel("Match a list of Mz")
+)
diff --git a/publish_rshinyapp.sh b/publish_rshinyapp.sh
@@ -2,10 +2,10 @@
 
 install.packages('rsconnect')
 
-library(devtools)
-library(roxygen2)
-document()
-install()
+#library(devtools)
+#library(roxygen2)
+#document()
+#install()
 
 library(rsconnect)
 
@@ -32,7 +32,6 @@ if ( nchar(APP_NAME)<=0 ) {
 
 install.packages("shiny")
 install.packages("DT")
-library(shiny)
-library(DT)
+devtools::install_github("p2m2/oligopeptides_matching")
 
-rsconnect::deployApp('oligopeptides_matching',appName=APP_NAME,forceUpdate = TRUE)
+rsconnect::deployApp('oligopeptides_matching',appName=APP_NAME,forceUpdate = TRUE)