update interface

GBrowser.R

@@ -87,7 +87,7 @@ GBrowser <- function(chr="chr07", start=29616705, end=29629223, accession=NULL,
  snpeff.reg.3 <- snpeff.reg.3[snpeff.reg.3$tag %in% mutType, , drop=FALSE]
  }
 
- p1 <- ggplot(data=snpeff.reg.3) + geom_point(aes(x=pos, y=yr, color=tag, text=info, fill=tag), size=0.8, pch=25)
+ p1 <- ggplot2::ggplot(data=snpeff.reg.3) + ggplot2::geom_point(ggplot2::aes(x=pos, y=yr, color=tag, text=info, fill=tag), size=0.8, pch=25)
 
 
  gff$id <- gsub(":.+", "", gff$id)
@@ -128,7 +128,7 @@ GBrowser <- function(chr="chr07", start=29616705, end=29629223, accession=NULL,
  })
  plot.nm <- do.call(rbind, plot.nm.lst)
  if (!is.null(plot.nm) && nrow(plot.nm)>0) {
- p1 <- p1 + geom_rect(aes(xmin=start, xmax=end, ymin=ymin, ymax=ymax), 
+ p1 <- p1 + ggplot2::geom_rect(ggplot2::aes(xmin=start, xmax=end, ymin=ymin, ymax=ymax), 
  color="grey30", fill="grey30", data=plot.nm)
  }
 
@@ -145,7 +145,7 @@ GBrowser <- function(chr="chr07", start=29616705, end=29629223, accession=NULL,
  })
  plot.mrna <- do.call(rbind, plot.mrna.lst)
  if (!is.null(plot.mrna) && nrow(plot.mrna)>0) {
- p1 <- p1 + geom_rect(aes(xmin=start, xmax=end, ymin=y+0.118, ymax=y+0.122), 
+ p1 <- p1 + ggplot2::geom_rect(ggplot2::aes(xmin=start, xmax=end, ymin=y+0.118, ymax=y+0.122), 
  color="grey30", fill="grey30", data=plot.mrna)
  }
 
@@ -191,24 +191,24 @@ GBrowser <- function(chr="chr07", start=29616705, end=29629223, accession=NULL,
  })
  plot.tail <- do.call(rbind, plot.tail.lst)
  if (!is.null(plot.tail) && nrow(plot.tail)>0) {
- p1 <- p1 + geom_polygon(aes(x=xx, y=yy, group=pare), color="grey30", fill="grey30", 
+ p1 <- p1 + ggplot2::geom_polygon(ggplot2::aes(x=xx, y=yy, group=pare), color="grey30", fill="grey30", 
  data=plot.tail)
  }
 
 
- p1 <- p1 + scale_y_continuous("", breaks=NULL)
- p1 <- p1 + theme(panel.grid.major=element_blank(),panel.grid.minor=element_blank()) + 
- theme(panel.background=element_rect(fill="white",colour="white"))
- p1 <- p1 + xlab("Chromosome position")
- p1 <- p1 + guides(color=guide_legend(title=NULL))
+ p1 <- p1 + ggplot2::scale_y_continuous("", breaks=NULL)
+ p1 <- p1 + ggplot2::theme(panel.grid.major=ggplot2::element_blank(), panel.grid.minor=ggplot2::element_blank()) + 
+ ggplot2::theme(panel.background=ggplot2::element_rect(fill="white",colour="white"))
+ p1 <- p1 + ggplot2::xlab("Chromosome position")
+ p1 <- p1 + ggplot2::guides(color=ggplot2::guide_legend(title=NULL))
 
- p1 <- p1 + guides(fill=FALSE)
+ p1 <- p1 + ggplot2::guides(fill=FALSE)
 
- p3 <- p1 + theme(axis.ticks.y = element_blank(), axis.text.y = element_blank(),
- axis.line.y = element_blank())
- p3 <- ggplotly(p3, tooltip = c("pos", "info"))
+ p3 <- p1 + ggplot2::theme(axis.ticks.y = ggplot2::element_blank(), axis.text.y = ggplot2::element_blank(),
+ axis.line.y = ggplot2::element_blank())
+ p3 <- plotly::ggplotly(p3, tooltip = c("pos", "info"))
 
- p3 <- p3 %>% layout(
+ p3 <- p3 %>% plotly::layout(
  title = "",
  xaxis = list(
  rangeselector = list(),
@@ -233,7 +233,7 @@ GBrowser <- function(chr="chr07", start=29616705, end=29629223, accession=NULL,
  }
  }
 
- p4 <- onRender(p3, "
+ p4 <- htmlwidgets::onRender(p3, "
  function(el, x) {
  el.on('plotly_click', function(d) {
  var url = d.points[0].customdata;

Global.R

@@ -2,24 +2,26 @@
 options(warn=-1)
 
 # library(IRanges)
- library(plotly)
- library(LDheatmap)
- library(chopsticks)
+# library(plotly)
+# library(LDheatmap)
+# library(chopsticks)
 # library(foreach)
 # library(ape)
 # library(pegas)
- library(plyr)
- library(dplyr)
+# library(plyr)
+library(dplyr)
 # library(ggmap)
- library(tidyr)
-library(gridExtra)
+# library(tidyr)
+# library(gridExtra)
 # library(ggtree)
-library(grid)
+# library(grid)
 library(snpStats)
-library(htmlwidgets)
+# library(htmlwidgets)
 # library(shinycssloaders)
 # library(shinysky)
 # library(shinyWidgets)
+# library(shinythemes)
+library(shinyBS)
 
 source("fetchSnp.R")
 source("ld.heatmap.R")
@@ -52,3 +54,10 @@ chrInfo <- read.table("./data/chrInfo.txt", head=T, as.is=T, sep="\t")
 
 acc.tree <- read.table("./data/acc.tree.txt", 
  head=T, as.is=T, sep="\t", row.names = 1)
+
+footerTagList <- list(
+ tags$footer(id = "myFooter",
+ shiny::includeHTML("www/footer.html")
+ )
+)
+

chooser.R

@@ -20,15 +20,15 @@ chooserInput <- function(inputId, leftLabel, rightLabel, leftChoices, rightChoic
  )),
  div(id=inputId, class="chooser",
  div(class="chooser-container chooser-left-container", 
- tags$select(class="left", size=size, multiple=multiple, leftChoices, style="width:185px;background:gray")
+ tags$select(class="left", size=size, multiple=multiple, leftChoices, style="width:185px;background:gray50")
  ),
  div(class="chooser-container chooser-center-container",
  icon("arrow-circle-o-right", "right-arrow fa-3x"),
  tags$br(),
  icon("arrow-circle-o-left", "left-arrow fa-3x")
  ),
  div(class="chooser-container chooser-right-container",
- tags$select(class="right", size=size, multiple=multiple, rightChoices, style="width:185px;background:gray")
+ tags$select(class="right", size=size, multiple=multiple, rightChoices, style="width:185px;background:gray50")
  )
  )
  )

geneStru.R

@@ -47,7 +47,7 @@ geneStru <- function(chr="chr09", start=37800, end=46400){
  return(dat.mrna)
  })
  plot.mrna <- do.call(rbind, plot.mrna.lst)
- p1 <- ggplot(plot.mrna) + geom_rect(aes(xmin=start, xmax=end, ymin=y+0.118, ymax=y+0.122,
+ p1 <- ggplot2::ggplot(plot.mrna) + ggplot2::geom_rect(ggplot2::aes(xmin=start, xmax=end, ymin=y+0.118, ymax=y+0.122,
  text=anno), 
  color="grey30", fill="grey30")
 
@@ -69,7 +69,7 @@ geneStru <- function(chr="chr09", start=37800, end=46400){
  })
  plot.nm <- do.call(rbind, plot.nm.lst)
  if (nrow(plot.nm)>0) {
- p1 <- p1 + geom_rect(aes(xmin=start, xmax=end, ymin=ymin, ymax=ymax, text=anno), 
+ p1 <- p1 + ggplot2::geom_rect(ggplot2::aes(xmin=start, xmax=end, ymin=ymin, ymax=ymax, text=anno), 
  color="grey30", fill="grey30", data=plot.nm)
  }
 
@@ -111,17 +111,17 @@ geneStru <- function(chr="chr09", start=37800, end=46400){
  return(dat.tail)
  })
  plot.tail <- do.call(rbind, plot.tail.lst)
- p1 <- p1 + geom_polygon(aes(x=xx, y=yy, group=pare), color="grey30", fill="grey30", 
+ p1 <- p1 + ggplot2::geom_polygon(ggplot2::aes(x=xx, y=yy, group=pare), color="grey30", fill="grey30", 
  data=plot.tail)
 
  snp.pos.df <- data.frame(x=snp.code.pos, ymin=1.23, ymax=1.25, stringsAsFactors = FALSE)
- p1 <- p1 + geom_linerange(aes(x=x, ymin=ymin, ymax=ymax), data=snp.pos.df)
- p1 <- p1 + geom_segment(aes(x=min(snp.code.pos), xend=max(snp.code.pos), y=1.25, yend=1.25))
+ p1 <- p1 + ggplot2::geom_linerange(ggplot2::aes(x=x, ymin=ymin, ymax=ymax), data=snp.pos.df)
+ p1 <- p1 + ggplot2::geom_segment(ggplot2::aes(x=min(snp.code.pos), xend=max(snp.code.pos), y=1.25, yend=1.25))
 
- p1 <- p1 + scale_y_continuous("", breaks=NULL)
- p1 <- p1 + theme(panel.grid.major=element_blank(),panel.grid.minor=element_blank()) + 
- theme(panel.background=element_rect(fill="white",colour="white"))
- p1 <- p1 + scale_x_continuous("", breaks=NULL)
+ p1 <- p1 + ggplot2::scale_y_continuous("", breaks=NULL)
+ p1 <- p1 + ggplot2::theme(panel.grid.major=ggplot2::element_blank(),panel.grid.minor=ggplot2::element_blank()) + 
+ ggplot2::theme(panel.background=ggplot2::element_rect(fill="white",colour="white"))
+ p1 <- p1 + ggplot2::scale_x_continuous("", breaks=NULL)
 
  return(p1)
 }

hapGeo.R

@@ -31,17 +31,17 @@ hapGeo <- function(haplotype=NULL) {
  showcountries = TRUE,
  showsubunits = TRUE,
  landcolor = "white",
- oceancolor = toRGB("gray90"),
+ oceancolor = plotly::toRGB("gray90"),
  subunitwidth = 1,
  countrywidth = 0.5,
  subunitcolor = "blue",
  countrycolor = "gray85"
  )
 
  plotly::plot_geo(dat, lat = ~Latitude, lon = ~Longitude, color = ~hap) %>%
- add_markers(
+ plotly::add_markers(
  hovertext = ~text
- ) %>% layout(title = 'Geographic distribution of rice accessions with different haplotypes', geo = g)
+ ) %>% plotly::layout(title = 'Geographic distribution of rice accessions with different haplotypes', geo = g)
 
 }
 

hapGeoStatic.R

@@ -25,9 +25,9 @@ hapGeoStatic <- function(haplotype=NULL) {
 
  load("./data/worldmap.RData")
 
- mp <- mp + geom_point(aes(x=Longitude, y=Latitude, color=hap), size=0.5, data=dat) + 
- scale_x_continuous("", breaks=NULL) + scale_y_continuous("", breaks=NULL) 
- mp <- mp + guides(color=guide_legend(title=NULL))
+ mp <- mp + ggplot2::geom_point(ggplot2::aes(x=Longitude, y=Latitude, color=hap), size=0.5, data=dat) + 
+ ggplot2::scale_x_continuous("", breaks=NULL) + ggplot2::scale_y_continuous("", breaks=NULL) 
+ mp <- mp + ggplot2::guides(color=ggplot2::guide_legend(title=NULL))
  mp
 }
 

ld.heatmap.R

@@ -97,21 +97,21 @@ ld.heatmap <- function(chr="chr09", start=37800, end=46400, snp.pos=c(1),
  dat.snp.mat <- as(dat, "SnpMatrix")
 
  if (gene) {
- ll <- LDheatmap(dat.snp.mat, snp.code.pos, 
+ ll <- LDheatmap::LDheatmap(dat.snp.mat, snp.code.pos, 
  flip=TRUE, title=NULL, ...)
 
  p1 <- geneStru(chr=chr, start=start, end=end)
 
  plot.new()
- llQplot2 <- LDheatmap.addGrob(ll, rectGrob(gp=gpar(col="white")), height=.3)
- pushViewport(viewport(x=0.483, y=ld.y, width=ld.w, height=.1))
+ llQplot2 <- LDheatmap::LDheatmap.addGrob(ll, grid::rectGrob(gp=grid::gpar(col="white")), height=.3)
+ grid::pushViewport(grid::viewport(x=0.483, y=ld.y, width=ld.w, height=.1))
 
- grid.draw(ggplotGrob(p1))
+ grid::grid.draw(ggplot2::ggplotGrob(p1))
  } else {
  if (flip) {
- LDheatmap(dat.snp.mat, snp.code.pos, flip=TRUE, title=NULL, ...)
+ LDheatmap::LDheatmap(dat.snp.mat, snp.code.pos, flip=TRUE, title=NULL, ...)
  } else {
- LDheatmap(dat.snp.mat, snp.code.pos, flip=FALSE, SNP.name = colnames(dat)[snp.pos], title=NULL, ...)
+ LDheatmap::LDheatmap(dat.snp.mat, snp.code.pos, flip=FALSE, SNP.name = colnames(dat)[snp.pos], title=NULL, ...)
  }
  }
 

nucDiv.R

@@ -51,8 +51,8 @@ nucDiv <- function(chr="chr07", nuc.start=2800000, nuc.end=2900000, step=10,
  div.group.df.1 <- div.group.df[, c("pos", groups)]
  div.group.df.2 <- div.group.df[, c("pos", numerator, denominator)]
 
- div.group.df.1.long <- gather(div.group.df.1, group, diversity, -pos)
- div.group.df.2.long <- gather(div.group.df.2, group, diversity, -pos)
+ div.group.df.1.long <- tidyr::gather(div.group.df.1, group, diversity, -pos)
+ div.group.df.2.long <- tidyr::gather(div.group.df.2, group, diversity, -pos)
 
  nuc.chr <- substr(chr, 4, 5)
  nuc.gene.info <- gene.info
@@ -61,28 +61,28 @@ nucDiv <- function(chr="chr07", nuc.start=2800000, nuc.end=2900000, step=10,
  nuc.gene.info$start>=as.numeric(nuc.start) &
  nuc.gene.info$end<=as.numeric(nuc.end), ]
 
- p1 <- ggplot(div.group.df.1.long) + geom_line(aes(x=pos, y=diversity, color=group))
- p1 <- p1 + xlab("") + ylab("Nucleotide diversity")
- p1 <- p1 + theme_classic() + ylim(-0.14, NA)
- p1 <- p1 + theme(legend.title = element_blank())
- p1 <- p1 + theme(legend.position="top")
+ p1 <- ggplot2::ggplot(div.group.df.1.long) + ggplot2::geom_line(ggplot2::aes(x=pos, y=diversity, color=group))
+ p1 <- p1 + ggplot2::xlab("") + ggplot2::ylab("Nucleotide diversity")
+ p1 <- p1 + ggplot2::theme_classic() + ggplot2::ylim(-0.14, NA)
+ p1 <- p1 + ggplot2::theme(legend.title = ggplot2::element_blank())
+ p1 <- p1 + ggplot2::theme(legend.position="top")
 
  if (nrow(nuc.gene.info)>=1) {
- p1 <- p1 + geom_rect(aes(xmin=start, xmax=end, ymin=-0.05, ymax=-0.07), color="grey40", data=nuc.gene.info)
- p1 <- p1 + geom_text(aes(x=(start+end)/2, y=-0.12, label=id), angle=50, size=2.5, data=nuc.gene.info)
+ p1 <- p1 + ggplot2::geom_rect(ggplot2::aes(xmin=start, xmax=end, ymin=-0.05, ymax=-0.07), color="grey40", data=nuc.gene.info)
+ p1 <- p1 + ggplot2::geom_text(ggplot2::aes(x=(start+end)/2, y=-0.12, label=id), angle=50, size=2.5, data=nuc.gene.info)
  }
 
- p1 <- p1 + theme(axis.ticks.x = element_blank(), axis.text.x = element_blank(),
- axis.line.x = element_blank())
+ p1 <- p1 + ggplot2::theme(axis.ticks.x = ggplot2::element_blank(), axis.text.x = ggplot2::element_blank(),
+ axis.line.x = ggplot2::element_blank())
 
  div.group.df.2$value <- div.group.df.2[,numerator]/div.group.df.2[,denominator]
 
- p2 <- ggplot(div.group.df.2) + geom_line(aes(x=pos, y=value))
- p2 <- p2 + xlab("genomic position") + ylab(paste0(numerator, "/", denominator))
- p2 <- p2 + theme_classic()
+ p2 <- ggplot2::ggplot(div.group.df.2) + ggplot2::geom_line(ggplot2::aes(x=pos, y=value))
+ p2 <- p2 + ggplot2::xlab("genomic position") + ggplot2::ylab(paste0(numerator, "/", denominator))
+ p2 <- p2 + ggplot2::theme_classic()
 
- gp1 <- ggplotGrob(p1)
- gp2 <- ggplotGrob(p2)
+ gp1 <- ggplot2::ggplotGrob(p1)
+ gp2 <- ggplot2::ggplotGrob(p2)
  maxWidth = grid::unit.pmax(gp1$widths[2:5], gp2$widths[2:5])
  gp1$widths[2:5] <- as.list(maxWidth)
  gp2$widths[2:5] <- as.list(maxWidth)