In EricLarG4/g4dbr: G4 biophysics database visualization and management

library(knitr)

# allows figure sizing within r chunck
# modified from http://michaeljw.com/blog/post/subchunkify/
subchunkify <- function(g, cap=NULL, fig_height=7, fig_width=5) {
  #g argument is the object to plot
  #cap is the figure caption
  g_deparsed <- paste0(deparse( #deparse turns function() {g} into string that Knitr can interpret
    function() {g}
  ), collapse = '')

  sub_chunk <- paste0("
  `","``{r sub_chunk_", floor(runif(1) * 10000), #give the generated sub-chunk a unique name
  ", fig.height=", fig_height, ", fig.width=", fig_width, ", fig.cap=", cap, ", echo=FALSE, message=FALSE, warning=FALSE, fig.align='center', dpi = 600}",
  "\n(", 
  g_deparsed
  , ")()",
  "\n`","``
  ")

  #knitr::knit() compiles the generated sub-chunk
  cat(knitr::knit(text = knitr::knit_expand(text = sub_chunk), quiet = TRUE))
}

Data

#Extract the selected oligonucleotides names to print as a comma separated string
if (length(selected.oligos.db()) > 1) { #if more than one oligo, then use plural
  selected.oligos <- paste("oligonucleotides", paste(selected.oligos.db()[1:length(selected.oligos.db())-1], collapse=", "), "and", selected.oligos.db()[length(selected.oligos.db())])
} else { #else use singular 
  selected.oligos <- paste("oligonucleotide", paste(selected.oligos.db(), collapse=", "))
}

This report was generated by g4dbr for the r selected.oligos on r Sys.Date().

#Document title takes selected oligonucleotides values
title_var <- paste(paste(selected.oligos.db(), collapse="/"), "report")

title: r title_var author: g4dbr date: r Sys.Date() output: word_document: reference_docx: word-styles-reference.docx

#table of oligonucleotides properties (pageable)
db.info <- db.info() %>%
  filter(oligo %in% selected.oligos.db()) %>% #only display selected oligos data
  select(c('oligo', 'sequence', 'submitted_by', 'depo.date', 'DOI'))

knitr::kable(db.info,
             caption = 'General oligonucleotide information',
             escape = F) #DOI parsed in HTML reports

Figures

CD

if (length(selected.oligos.db()) > 1) {
  subchunkify(g = p.CD.db() +
                theme(legend.position = 'bottom',
                      legend.text = element_text(size = 8),
                      legend.title = element_text(size = 9)), #plot
              cap = "paste('Circular dichroism spectra of', paste('the', paste(selected.oligos.db()[1:length(selected.oligos.db())-1], collapse=', '), 'and', selected.oligos.db()[length(selected.oligos.db())]), 'oligonucleotides')", #figure caption
              fig_height = 3 * row.p.CD.db(), #dynamic figure height
              fig_width = 6.26
  ) 
} else {

  #Extraction of the oligo concentration
  conc.cd <- db.cd.select() %>%
  group_by(oligo) %>%
  filter(oligo == selected.oligos.db()) %>%
  ungroup() %>%
  select(con) %>%
  unique() %>%
  as.numeric()

  #Extraction of the path length
  path.cd <- db.cd.select() %>%
  group_by(oligo) %>%
  filter(oligo == selected.oligos.db()) %>%
  ungroup() %>%
  select(l) %>%
  unique() %>%
  as.numeric()

  subchunkify(g = p.CD.db()+
                guides(shape = FALSE) +
                theme(legend.position = 'bottom',
                      legend.text = element_text(size = 8),
                      legend.title = element_text(size = 9)), 
              cap = "paste0('Circular dichroism spectra of', paste(' the', paste(selected.oligos.db(), collapse=', ', 'oligonucleotide')), ' (', conc.cd, ' μM)', ', acquired at 25°C in ', path.cd, '-cm path length cuvettes')",
              fig_height = 3 * row.p.CD.db(), #dynamic figure height
              fig_width = (8*col.p.CD.db())/(col.p.CD.db()+0.5) #dynamic figure width
  )
}

1H-NMR

if (length(selected.oligos.db()) > 1) {
  subchunkify(g = p.NMR.db() +
                theme(legend.position = 'bottom',
                      legend.text = element_text(size = 8),
                      legend.title = element_text(size = 9)), #plot
              cap = "paste('1H-NMR spectra of the', paste(selected.oligos.db()[1:(length(selected.oligos.db())-1)], collapse = ', '), 'and', selected.oligos.db()[length(selected.oligos.db())], 'oligonucleotides, acquired at 25°C')", #figure caption
              fig_height = 4 * row.p.NMR.db(), #dynamic figure height
              fig_width = (9*col.p.NMR.db())/(col.p.NMR.db()+0.4) #dynamic figure width
  ) 
} else {
  subchunkify(g = p.NMR.db()+
                theme(legend.position = 'none'), 
              cap = "paste('1H-NMR spectrum of', paste('the', paste(selected.oligos.db(), collapse=', ', 'oligonucleotide,')), 'acquired at 25°C')",
              fig_height = 4 * row.p.NMR.db(), #dynamic figure height
              fig_width = (9*col.p.NMR.db())/(col.p.NMR.db()+0.4) #dynamic figure width
  )
}

UV-melting

Raw data

puf <- p.UV.fit.db() + 
  # guides(colour=guide_legend(nrow=length(selected.oligos.db()))) +
  theme(
    legend.text = element_text(size = 8),
    legend.title = element_text(size = 9),
    legend.direction = 'vertical')

if (length(selected.oligos.db()) > 1) {
  subchunkify(g = puf, #plot
              cap = "paste('Raw UV-melting plots of', paste('the', paste(selected.oligos.db()[1:length(selected.oligos.db())-1], collapse=', '), 'and', selected.oligos.db()[length(selected.oligos.db())]), 'oligonucleotides', 'acquired at 295 nm')", #figure caption
              fig_height = 4,
              fig_width = 6.26
  ) 
} else {
  subchunkify(g = puf, 
              cap = "paste('Raw UV-melting plots of', paste('the', paste(selected.oligos.db(), collapse=', ', 'oligonucleotide')), 'aquired at 295 nm')",
              fig_height = 4,
              fig_width = 6.26
  )
}

Processed data

puv <- p.UV.melting.db() + 
  # guides(colour=guide_legend(nrow=length(selected.oligos.db()))) +
  theme(
    legend.text = element_text(size = 8),
    legend.title = element_text(size = 9),
    legend.direction = 'vertical')

if (length(selected.oligos.db()) > 1) {
  subchunkify(g = puv, #plot
              cap = "paste('Folded fraction from UV-melting experiments at 295 nm of', paste('the', paste(selected.oligos.db()[1:length(selected.oligos.db())-1], collapse=', '), 'and', selected.oligos.db()[length(selected.oligos.db())]), 'oligonucleotides')", #figure caption
              fig_height = 4,
              fig_width = 6.26
  ) 
} else {
  subchunkify(g = puv, 
              cap = "paste('Folded fraction from UV-melting experiments at 295 nm of', paste('the', paste(selected.oligos.db(), collapse=', ', 'oligonucleotide')))",
              fig_height = 4,
              fig_width = 6.26
  )
}

#controls whether MS section is knitted or not based on the use of the plotMS button
if(input$plotMS.db == 0) {
  print.option <- FALSE
} else {
  print.option <- TRUE
}

#conditional MS section title
asis_output("## Native ESI-MS")

pms <- p.MS.db() + 
  theme(legend.position="bottom",
        legend.direction = 'horizontal',
        legend.text = element_text(size = 8),
        legend.title = element_text(size = 9))

if (length(selected.oligos.db()) > 1) {
  subchunkify(g = pms, #plot
              cap = "paste('Native ESI-MS spectra of', paste('the', paste(selected.oligos.db()[1:length(selected.oligos.db())-1], collapse=', '), 'and', selected.oligos.db()[length(selected.oligos.db())]), 'oligonucleotides')", #figure caption
              fig_height = 3 * row.p.MS.db(), #dynamic figure heights
              fig_width = (9*col.p.MS.db())/(col.p.MS.db()+0.4) #dynamic figure width
  ) 
} else {
  subchunkify(g = pms, 
              cap = "paste('Native ESI-MS spectra of', paste('the', paste(selected.oligos.db(), collapse=', ', 'oligonucleotide')))",
              fig_height = 3 * row.p.MS.db(), #dynamic figure height
              fig_width = (9*col.p.MS.db())/(col.p.MS.db()+0.4) #dynamic figure width
  )
}