Some (alt)metrics of Aalto University publications since 2010 as a Shiny application

aalto_since2010.csv

getdata.R

###########################################################
#
# Altmetrics data provided by Altmetric.com
# Web of Science data provided by Thomson Reuters
#
# 1. get data from local db
# 2. search Altmetric.com
# 3. merge
#
##########################################################
library(RPostgreSQL)
library(rAltmetric)
library(plyr)
library(reshape)


drv <- dbDriver("PostgreSQL")
con <- dbConnect(drv, user = "xxx", password = "xxxxx", dbname = "xxxx", host = "xxxx", port = xxxx)

# Fetch data by School to *.doi dataframes with 'dbGetQuery' SQL commands. Not shown here.

dbDisconnect(con)
dbUnloadDriver(drv)

# Merge DOIs (and other variables) by school 
aalto.doi <- merge_all(list(arts.doi, biz.doi, chem.doi, elec.doi, eng.doi, sci.doi))
# Preamble DOIs for the rAltmetric run
aalto.doi$di <- paste("doi/", aalto.doi$di, sep = "")
write.csv(aalto.doi, file = "aalto_metrics_2010.csv")

# Pull out just the DOIs
dois <- as.data.frame(aalto.doi$di, stringsAsFactors = FALSE)
# Rename the variable
names(dois) <- c("doi")

# Query Altmetric API with rAltmetric
raw_metrics <- llply(dois$doi, altmetrics, .progress = 'text')
metric_data <- ldply(raw_metrics, altmetric_data)

write.csv(metric_data, file = "aalto_metric_2010.csv")

# Merge with local data
aalto.doi$di <- sub("doi/", "", aalto.doi$di)
aalto.all.m <- merge(metric_data, aalto.doi, by.x = "doi", by.y = "di")

aalto.all <- aalto.all.m[ , c("doi", 
                              "school",
                              "ti",
                              "au",
                              "url", 
                              "details_url", 
                              "py",
                              "j9",
                              "so",
                              "tc", 
                              "score",
                              "mendeley", 
                              "connotea", 
                              "citeulike", 
                              "readers_count",
                              "cited_by_gplus_count", 
                              "cited_by_fbwalls_count",
                              "cited_by_posts_count", 
                              "cited_by_tweeters_count",
                              "cited_by_accounts_count", 
                              "cited_by_feeds_count", 
                              "cited_by_videos_count",
                              "cited_by_delicious_count",
                              "cited_by_rdts_count",
                              "cited_by_forum_count",
                              "cited_by_qs_count",
                              "cited_by_rh_count",
                              "cited_by_msm_count")]

write.csv(aalto.all, file = "aalto_since2010.csv", row.names = FALSE)

global.R

library(shiny)
library(ggplot2)
library(rCharts)
library(reshape2)
library(stringr)
library(ggvis)


# Few lines with double quotes inside fields terminated by quotes
# sed -i 's/""/%%/g' aalto_since2010.csv 

aalto_all_m <- read.table(file = "aalto_since2010.csv", 
                          header = TRUE, 
                          sep = ",",
                          col.names = c("DOI", "School", "Title", "Authors", "URL", 
                                        "Altmetric.com_URL", "Year", "Journal_short", "Journal_long",
                                        "WoS", "Altmetric", "Mendeley", "Connotea", "CiteULike",
                                        "Readers_count", "GooglePlus", "Facebook", "Any_type_of_posts", "Twitter", 
                                        "Accounts", "Blog_posts", "Videos", "Delicious_bookmarks", 
                                        "Reddit", "Forums",
                                        "StackExchange", "rh",                                     
                                        "Science_news_outlets"),
                          colClasses = c("character", "character", "character", "character", "character",
                                         "character", "character", "character", "character",
                                         "integer", "numeric", "integer", "integer", "integer",
                                         "integer", "integer", "integer", "integer", "integer", 
                                         "integer", "integer", "integer", "integer", 
                                         "integer", "integer", 
                                         "integer", "integer",
                                         "integer"),
                          stringsAsFactors = FALSE)


# Readers_count = Mendeley + CiteULike; rh = ?
aalto_all_m <- aalto_all_m[ ,c("DOI", "School", "Title", "Authors", "URL", 
                               "Altmetric.com_URL", "Year", "Journal_short", "Journal_long",
                               "WoS", "Altmetric", "Mendeley", "Connotea", "CiteULike",
                               "GooglePlus", "Facebook", "Twitter", 
                               "Accounts", "Blog_posts", "Videos", "Delicious_bookmarks", 
                               "Reddit", "Forums",
                               "StackExchange", "rh",                                     
                               "Science_news_outlets")]

names(aalto_all_m) <- c("DOI", "School", "Title", "Authors", "URL", 
                        "AltmetricURL", "Year", "Journal short", "Journal",
                        "WoS", "Altmetric", "Mendeley", "Connotea", "CiteULike",
                        "GooglePlus", "Facebook", "Twitter", 
                        "Accounts", "Blog posts", "Videos", "Delicious", 
                        "Reddit", "Forums","StackExchange", "rh", "NewsOutlets")

# Altmetric.com_score value to ceiling 
aalto_all_m$Altmetric <- as.integer(ceiling(aalto_all_m$Altmetric))

# In original data, we have duplicate DOIs if the article is co-authored by
# multiple Schools. Here, we deliberately delete that information, and
# the DOI is randomnly put under one of the Schools
aalto_all <- aalto_all_m[!duplicated(aalto_all_m$DOI),]

# Some Altmetric.com data is NA, some 0
aalto_all[is.na(aalto_all)] <- ""

# See remark on top
aalto_all$Title <- with(aalto_all, gsub("%%", "'", Title))

# For unknown reason, some columns need to be transformed twice to integer 
columns <- c(which(colnames(aalto_all) == "GooglePlus"):ncol(aalto_all))
aalto_all[ ,columns] <- apply(aalto_all[ ,columns], 2, function(x) as.integer(as.character(x)))

# See ?toupper
simpleCap <- function(x) {
  s <- strsplit(x, " ")[[1]]
  paste(toupper(substring(s, 1,1)), substring(s, 2),
        sep="", collapse=" ")
}

aalto_all$Journal <- sapply(aalto_all$Journal, tolower)
aalto_all$Journal <- sapply(aalto_all$Journal, function(x) simpleCap(x))

# Acronyms for plot labels and tooltips
aalto_all$Title5 <- with(aalto_all, paste(substring(Title,1,5), " (", Year, ")", sep=""))
aalto_all$Title20 <- with(aalto_all, paste(substring(Title,1,20), " (", Year, ")", sep=""))
#aalto_all$Authors5 <- with(aalto_all, paste(substring(Authors,1,5), " (", Year, ")", sep=""))
aalto_all$Journal5 <- with(aalto_all, paste(substring(Journal,1,5), " (", Year, ")", sep=""))

# Number of authors
aalto_all$NrOfAuthors <- with(aalto_all, as.integer(str_count(Authors, ";")+1))
# Keys for ggvis tooltips
aalto_all$keys <- seq_along(aalto_all[,1])

metrics <- c("Altmetric", "WoS", "Mendeley", "Twitter", "Facebook", "GooglePlus", "CiteULike", 
             "Videos", "Reddit", "NewsOutlets", "NrOfAuthors")

dimensions <- c("Title", "Journal")

colsPlot <- c("Altmetric", "WoS", "Mendeley", "Twitter", "Facebook", "GooglePlus", "CiteULike", 
              "Videos", "Reddit", "NewsOutlets", "School", "Year", "Title5", "Journal5", "NrOfAuthors")

colsChart <- c("Altmetric", "WoS", "Mendeley", "Twitter", "Facebook", "GooglePlus", "CiteULike", 
               "Videos", "Reddit", "NewsOutlets", "id", "NrOfAuthors")

colsTable <- c("Journal", "Title", "AltmetricURL", "NrOfAuthors", "Altmetric",
               "Authors", "Year", "WoS", "Mendeley", "School",
               "Twitter", "Facebook", "GooglePlus", "CiteULike",
               "Videos", "Reddit", "NewsOutlets")

schools <- "ARTS = School of Arts, Design and Architecture
    <br/>BIZ = School of Business<br/>CHEM = School of Chemical Technology<br/>ELEC = School of Electrical Engineering<br/>ENG = School of Engineering
    <br/>SCI = School of Science"

server.R

shinyServer(function(input, output, session) {
  
  
  output$text <- renderText({
    
    "Data as of 30th June 2014, by Altmetric and Thomson Reuters. <br/><br/>
    For more details, see this <a href='https://blogs.aalto.fi/suoritin/2014/06/30/new-take-in-recent-altmetrics/' target='_blank'>blog posting</a>, and the
    <a href='https://gist.github.com/tts/5df86b664b840c5927f9' target='_blank'>R code</a>"
    
  })
  
  output$text2 <- renderText({
    
    "Altmetric = Altmetric score <br/> NrOfAuthors = Number of authors<br/>WoS = Thomson Reuters Web of Science citations <br/><br/>
    For other metrics, see <a href='http://api.altmetric.com/docs/call_citations.html' target='_blank'>Altmetric API documentation</a>"
    
  })
  
  output$ggplot2schools <- renderText({schools})
  output$nvd3schools <- renderText({schools})
  output$gvschools <- renderText({schools})

  
  # Render a selectize drop-down selection box 
  output$items <- renderUI({
    
    if ( input$dim == 'Title') {
      nr <- 10
    } else {
      nr <- 5
    }
    
    selectizeInput(
      inputId = 'items', 
      label = paste0('Select max ', nr, '. Click to delete'),
      multiple = TRUE,
      choices = aalto_all[ ,names(aalto_all) %in% input$dim],
      options = list(maxItems = nr, placeholder = 'Start typing'),
      width = '400px'
    )
    
  })
  
  
  # Render a selection box for choosing X coord
  output$coordx <- renderUI({
    
    selectInput(
      inputId = 'xc', 
      label = 'Metrics for X',
      choices = as.list(metrics),
      selected = c("WoS")
    )
    
  })
  
  # and the Y coord
  output$coordy <- renderUI({
    
    selectInput(
      inputId = 'yc', 
      label = 'Metrics for Y',
      choices = as.list(metrics),
      selected = c("Mendeley")
    )
    
  })
  
  items <- reactive({
    
    if(is.null(input$items)){
      return()
    }
    
    df <- aalto_all[aalto_all[[input$dim]] %in% input$items, ]
    df
    
  })
  
  
  # Output to Plot tab with ggplot2
  output$plot <- renderPlot({
    
    validate(
      need(!is.null(items()), paste0("Please select some items from ", input$dim, "."))
    )
    
    data <- items()
    data <- data[, c(names(data) %in% colsPlot)]
    nr <- nrow(data)
    xval <- input$xc
    yval <- input$yc
    
    
    validate(
      need(nrow(data[data[[xval]] == '',]) < nr, 
           paste0("No ", xval, " data. Please select another metrics for X")),
      need(nrow(data[data[[yval]] == '',]) < nr, 
           paste0("No ", yval, " data. Please select another metrics for Y"))
    )     
    
    p <- ggplot(data, aes_string(x = xval, y = yval)) + 
      geom_point(aes(colour = School), size = 3) + 
      theme_bw() + 
      geom_text(aes_string(label=paste0(input$dim,'5')), size=3, vjust=0, hjust=-0.1) 
    
    
    print(p)
    
  })
  
  
  # Output to Chart tab with rCharts/NVD3
  output$chart <- renderChart({
    
    validate(
      need(!is.null(items()), paste0("Please select some items from ", input$dim, "."))
    )
    
    if(nrow(items()) == 0){
      return()
    }
    
    dataC <- items()
    dataC$id <- substr(dataC$AltmetricURL, 47, nchar(dataC$AltmetricURL))
    dataCsub <- dataC[, c(names(dataC) %in% colsChart)]
    
    # Transform data for plotting
    dataM <- melt(dataCsub, id.vars="id")
    nplot <- nPlot(value ~ id, data = dataM, group = "variable", type = "multiBarChart")
    nplot$chart(reduceXTicks = FALSE)
    nplot$xAxis(staggerLabels = TRUE)
    nplot$set(dom="chart")
    return(nplot)
    
  })
  
  # http://stackoverflow.com/a/24557912/2613636
  selected <- reactive({
    if (is.null(input$items)) {
      return(aalto_all)
    }
    df <- items()
    #df <- aalto_all[aalto_all[[input$dim]] %in% input$items, ]
    df$keys <-seq_along(df[,1])
    if(nrow(df) == 0){
      return(aalto_all)
    }
    df
  })
  
  #prop(x = input_select(c("disp", "wt")), constant = FALSE)
  
  selected %>% 
    ggvis(~WoS, ~NrOfAuthors, fill = ~School, key := ~keys) %>%
    layer_points() %>%
    add_tooltip(show_title) %>%
    bind_shiny("gv")
  
  
  show_title <- function(x=NULL) {
    if(is.null(x)) return(NULL)
    key <- x["keys"][[1]]
    paste0(selected()$Title20[key], " ", selected()$Journal[key])
  }  
  
  
  # Output nr of items to Table tab
  output$rownr <- renderText({
    
    paste("Number of items: ", if (is.null(items())) { "0" } else { nrow(items()) })
    
  })
  
  
  # Output to Table tab
  output$table <- renderTable({
    
    if (is.null(items()))
      return(invisible())
    
    rows <- items()
    rows <- rows[, c(names(rows) %in% colsTable)]
    
    # Shorten Authors and make URL of the Altmetric landing page
    for (i in 1:nrow(rows)) {
      au <- paste0(substr(rows$Authors[i], 1, 30), "...")
      rows[i, c("Authors")] <- au
      url <- substr(rows$AltmetricURL[i], 47, nchar(rows$AltmetricURL[i]))
      doUrl <- paste("<a href=", rows[i, c("AltmetricURL")], "\" target=\"_blank\">", url, "</a>", sep = "")
      rows[i, c("AltmetricURL")] <- doUrl
    } 
    return(rows)
    
    
  }, include.rownames = FALSE, sanitize.text.function = function(s) s)  
  
  
})

ui.R

shinyUI(fluidPage(
  
  titlePanel('Some (alt)metric data for Aalto University articles published since 2010'),
  
  sidebarLayout(
    sidebarPanel(
      selectInput(
        inputId = "dim", 
        label = "Dimension", 
        choices = c("Title", "Journal")
      ),
      uiOutput("items"),
      br(),
      uiOutput("coordx"),
      uiOutput("coordy"),
      br(),
      "Selection of X and Y affects only the first chart.",
      br(),
      br(),
      htmlOutput("text")
      ),
    
    
    mainPanel(
      
      tabsetPanel(
        tabPanel("Compare two metrics", plotOutput("plot"),
                 br(),
                 htmlOutput("ggplot2schools")),
        tabPanel("All metrics", showOutput("chart", "nvd3"),
                 br(),
                 htmlOutput("text2")),
        tabPanel("WoS and nr of authors", ggvisOutput("gv"),
                 br(),
                 paste0("With no selected items, shows all ", nrow(aalto_all), " publications"),
                 br(),br(),
                 htmlOutput("gvschools")
                 ),
        tabPanel("Data", 
                 textOutput("rownr"),
                 br(),
                 tableOutput("table"))
      )
    )
  )
))