Development

[jennahamlin]

• Input of phylogenetic trees - Is RAxML trees the only input tree used?

[jennahamlin]

regarding the above comment - one mechanism for dealing with this, is using the accept function in fileInput. link explaining how the accept function when included only allows the specified files to be 'seen' in the file upload in the web browser (but not in the rstudio version)

Need to maybe include a help text here, explaining what the data file/structure should be.

[jennahamlin]

link to basic treeviewer shiny app - poke around and adjust to what looks good

[jennahamlin]

Current state both via my personal workstation and now available on internal network

Completed

• upload metafile
• upload genetic distance
• reactive input for multiple parameters for tree viewing (align tips, font, tree format, size of scale bar, bootstrap cutoff, midpoint root).

Working on

• download adjusted tree image
• can use the brushPoints function but want it to display the tips brushed
• port over brushed tips and apply cladeLabel function to annotate

[jennahamlin]

State of package -

Completed

• download adjusted tree image module
• can displays tips brushed
• displays the combined tree and genetic distance info

Working on

• [ ] displays snp differences between two selected tips

• [x] incorporate brushed tips to apply cladeLabel function

minor issues

• [ ] bootstrap support shows values 1 - 9 instead of not displaying them

• [x] header repeated as first row in csv or tsv

[jennahamlin]

• still strange file name saved on ubuntu and pdf but correct file name for png or tiff. unclear of why this is happening

• [x] still strange file input for genetic distance. skips column name for first column

[jennahamlin]

• displays snp differences for all comparisons in a melted dataframe based on the input brush

• need to subset that to only include the labels selected

[jennahamlin]

moved brush selection and table display out to another module

[jennahamlin]

able to grab node for cladelabels using a function and can annotate the tree but still un able to place brushedPoints selected tips into the vector..

[jennahamlin]

Completed

• unlimited brushed tips selection to add annotation

Issues

• annotation generates multiple duplicate layers of base tree - need to only display one layer

To Do

• Add function to calculate number of SNPs and display that within the annotation
• Disconnect tree visualization from genetic distance upload; so that tinsel is also just a basic tree visualization tool
• Reconnected annotated tree with image download module
• module for counting number of tree images downloaded - probably by having user put in their name or contact info

[jennahamlin]

Completed

• annotation generates multiple duplicate layers of base tree - need to only display one layer

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored

To Do

• Add function to calculate the number of SNPs and display that within the annotation
• function or button to place annotations in specific locations
• Disconnect tree visualization from genetic distance upload; so that tinsel is also just a basic tree visualization tool
• Reconnected annotated tree with image download module
• module for counting the number of tree images downloaded - probably by having user put in their name or contact info

[jennahamlin]

User input thoughts -

• clear brushed selection in UI as a possible mechanism to deal with accidental selection

• check if annotation is already there before plotting

• routine for updating or annotation; click brush stroke in ui and look to see if annotation of clade and trigger update

[jennahamlin]

Completed

• reconnected tree viz parameter changes with annotation module
• added a reset to base tree button

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored
• need to move the annotation line over into empty space of plot

To Do

• Add function to calculate the number of SNPs and display that within the annotation function or button to place annotations in specific locations
• Disconnect tree visualization from genetic distance upload; so that tinsel is also just a basic tree visualization tool
• Reconnect annotated tree with image download module
• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info

[jennahamlin]

Completed

• Reconnected annotated tree with image download module

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored
• can move the annotation line over into empty space of plot but still not perfect

To Do

• Add function to calculate the number of SNPs and display that within the annotation function or button to place annotations in specific locations
• Disconnect tree visualization from genetic distance upload; so that tinsel is also just a basic tree visualization tool
• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network

[jennahamlin]

Completed

• Disconnected tree visualization from genetic distance upload; so that tinsel is also just a basic tree visualization tool

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored
• can move the annotation line over into empty space of plot - improved - but still not perfect
• reset aka remove annotations is not working

To Do

• Add function to calculate the number of SNPs and display that within the annotation function or button to place annotations in specific locations
• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network
• add the ability to upload a new tree file without having to close the application

[jennahamlin]

Completed

• added the ability to upload a new tree file without having to close the application
• annotation placement looks okay to me

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored
• reset aka remove annotations is not working - attempted shinyjs, but didn't work need to fiddle a bit more with it
• when uploading a new tree without closing the application, unable to add annotations to tree

To Do

• Add function to calculate the number of SNPs and display that within the annotation function or button to place annotations in specific locations
• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue

[jennahamlin]

updated website with better documentation for Shiny

[jennahamlin]

Issue

bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored

treein <- treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")

str(treein)

#this put an NA in first value, instead of leaving blank
# bs <- as.numeric(treein$node.label)%>%  
  sprintf("%02s",.) 

bs <- ifelse((nchar(treein$node.label)!=2 &!is.na(as.numeric(treein$node.label))) ,paste0("0",treein$node.label),treein$node.label)

treein2<-purrr::list_modify(treein, node.label = bs)

str(treein2)

treein2$node.label

This does what I want in R but when I put into shiny, I get an error (NA's introduced) and R aborts.

[jennahamlin]

getting snp differences to calculate mean and median based on tips selected

##get mean and median of snp differences  

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)

#this will pull out the value for column1, and column2
geneFile3 %>% 
  dplyr::filter(label == geneFile3$label[1] & name == geneFile3$name[2]) %>% 
  dplyr::pull(value)

#this will pull snp differences using labels
geneFile3 %>% 
  dplyr::filter(label == "2015C-3893_fastx5" & name == "PNUSAE000514_fastx5") %>% 
  dplyr::pull(value)

#this will pull out snp differences based on coordinates in character vector of tips
tips<-c("2015C-3893_fastx5", "PNUSAE000514_fastx5")

geneFile3 %>% 
  dplyr::filter(label == tips[1] & name == tips[2]) %>% 
  dplyr::pull(value)

#using three variables in character vector called tips
tips<-c("2015C-3893_fastx5", "PNUSAE000514_fastx5", "PNUSAE000634_fastx5")

#I can loop through and compare each variable in tips to the list isolate
for (i in 1:length(tips)) {
  geneFile3%>%
    dplyr::filter(label == tips[i] & name == "PNUSAE000514_fastx5") %>% 
    print(dplyr::pull(value))
}

for (i in 1:length(tips)) {
 for (j in 2:length(tips)){
+   tipVector<-geneFile3%>%
+     dplyr::filter(label == tips[i] & name == tips[j]) %>% 
+     print(dplyr::pull(value))
+   print(tipVector)
+   }}
# A tibble: 1 x 3
  label             name                value
  <chr>             <chr>               <chr>
1 2015C-3893_fastx5 PNUSAE000634_fastx5 1    
# A tibble: 1 x 3
  label             name                value
  <chr>             <chr>               <chr>
1 2015C-3893_fastx5 PNUSAE000634_fastx5 1    
# A tibble: 1 x 3
  label               name                value
  <chr>               <chr>               <chr>
1 PNUSAE000514_fastx5 PNUSAE000634_fastx5 2    
# A tibble: 1 x 3
  label               name                value
  <chr>               <chr>               <chr>
1 PNUSAE000514_fastx5 PNUSAE000634_fastx5 2    
# A tibble: 1 x 3
  label               name                value
  <chr>               <chr>               <chr>
1 PNUSAE000634_fastx5 PNUSAE000634_fastx5 0    
# A tibble: 1 x 3
  label               name                value
  <chr>               <chr>               <chr>
1 PNUSAE000634_fastx5 PNUSAE000634_fastx5 0    

**output is repeated twice and are seperate lists**
for (i in 1:length(tips)) {
  for (j in 2:length(tips)){
  tipVector<- geneFile3%>%
    dplyr::filter(label == tips[i] & name == tips[j]) %>% 
    dplyr::pull(value)
  print(tipVector)
}
}
[1] "1"
[1] "1"
[1] "0"
[1] "2"
[1] "2"
[1] "0"

[jennahamlin]

Completed

• added a remove last annotation button. Can remove all except the first placed annotation.

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree

To Do

• Add function to calculate number of SNPs and display within the annotation function
• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation.

[jennahamlin]

getting snp differences to calculate mean and median based on tips selected - continued

##get mean and median of snp differences  

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)

#using three variables in character vector called tips
 tips<-c("2015C-3893_fastx5", "PNUSAE000514_fastx5", "PNUSAE000634_fastx5")

tipVector <- c()

for (i in 1:length(tips)){
  for (j in 1:length(tips)){
    tipVector[i]<- geneFile3%>%
      dplyr::filter(label == tips[i] & name == tips[j]) %>%
      dplyr::pull(value)
    return(tipVector)
     }
}

**output**
mean(as.numeric(tipVector))
[1] 1
> tipVector
[1] "1" "2" "0" 

I believe this is what I want. Now need to incorporate it shiny.

[jennahamlin]

getting snp differences to calculate mean and median based on tips selected - continued - this will plot the mean snp differences for one monophyletic clade

library(shiny)
library(treeio)
library(ggtree)
library(phytools)
library(ape)

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)

##read in tree file 
treeFile <-treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")

tree_plot <-
  ggtree::ggtree(treeFile) +
  ggtree::geom_tiplab() +
  ggplot2::xlim(NA, 0.02)

tree_plot

##using a single monophyletic clade
tips<-c("2015C-3893_fastx5", "PNUSAE000514_fastx5")
tip_vector<-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"))

str(tip_vector)

snpVector <- c()

 for (i in 1:length(tips)){
   for (j in 1:length(tips)){
     snpVector[i]<- geneFile3%>%
       dplyr::filter(label == tips[i] & name == tips[j]) %>%
       dplyr::pull(value)
   }
 }

mean(as.numeric(snpVector))

make_layer <- function(tree, tips, label, color) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color
  )
}

#adjust lapply here to 1:2 when testing for two annotations with snp means
tree_plot + lapply(1, function(i)
     make_layer(
         tree_plot,
         tips = tip_vector[[i]],
         label = paste("Clade", i, mean(as.numeric(snpVector))),
         color = "red"
       ))

[jennahamlin]

getting snp differences to calculate mean based on tips selected - continued

this will plot the mean snp differences for >1 monophyletic clade

next up to combine with the plotting of annotations.

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)
############### now to get it to work for more than one label 
tip_vector<-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"),c("2015C-3777_fastx5", "2015C-3506_fastx5"))

snpVector <- c()

snp_anno <- function(geneFile, tips){ 
  for (i in 1:length(tips)){
    for (j in 1:length(tips)){
      snpVector[i]<- geneFile%>%
        dplyr::filter(label == tips[i] & name == tips[j]) %>%
        dplyr::pull(value)
    }
  }
  return(as.numeric(snpVector))
}

snpMean <-lapply(1:2, function(i)
  snp_anno(geneFile = geneFile3,
           tips= tip_vector[[i]]))

str(snpMean)

lapply(snpMean, mean)

## not incorporated yet
make_layer <- function(tree, tips, label, color) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color
  )
}

#adjust lapply here to 1:2 when testing for two annotations with snp means
tree_plot + lapply(1:2, function(i)
  make_layer(
    tree_plot,
    tips = tip_vector[[i]],
    label = paste("Clade", i),
    color = "red"
  ))

[jennahamlin]

getting snp differences to calculate mean based on tips selected - continued

issue need to have a filter to exclude self vs self rows in the genetic distance long dataframe

library(shiny)
library(treeio)
library(ggtree)
library(phytools)
library(ape)

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)

##read in tree file 
treeFile <-treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")

tree_plot <-
  ggtree::ggtree(treeFile) +
  ggtree::geom_tiplab() +
  ggplot2::xlim(NA, 0.02)

tree_plot

##using a single monophyletic clade
tips<-c("2015C-3893_fastx5", "PNUSAE000514_fastx5")
tip_vector<-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"))

str(tip_vector)

snpVector <- c()

 for (i in 1:length(tips)){
   for (j in 1:length(tips)){
     snpVector[i]<- geneFile3%>%
       dplyr::filter(label == tips[i] & name == tips[j]) %>%
       dplyr::pull(value)
   }
 }

mean(as.numeric(snpVector))

make_layer <- function(tree, tips, label, color) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color
  )
}

#adjust lapply here to 1:2 when testing for two annotations with snp means
tree_plot + lapply(1, function(i)
     make_layer(
         tree_plot,
         tips = tip_vector[[i]],
         label = paste("Clade", i, mean(as.numeric(snpVector))),
         color = "red"
       ))

############### now to get it to work for more than one label 
tip_vector<-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"),c("2015C-3777_fastx5", "2015C-3506_fastx5"))

snpVector <- c()

snp_anno <- function(geneFile, tips){ 
  for (i in 1:length(tips)){
    for (j in 1:length(tips)){
      snpVector[i]<- geneFile%>%
        dplyr::filter(label == tips[i] & name == tips[j]) %>%
        dplyr::pull(value)
    }
  }
  return(as.numeric(snpVector))
}

snpMean <-lapply(1:2, function(i)
  snp_anno(geneFile = geneFile3,
           tips= tip_vector[[i]]))

str(snpMean)

lapply(snpMean, mean)

make_layer <- function(tree, tips, label, color) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color
  )
}

#adjust lapply here to 1:2 when testing for two annotations with snp means
tree_plot + lapply(1:2, function(i)
  make_layer(
    tree_plot,
    tips = tip_vector[[i]],
    label = paste("Clade", i, lapply(snpMean[i], mean)),
    color = "red"
  ))

[jennahamlin]

Completed

• Generated function to calculate mean of SNPs and displays within the annotation - works in local R but need to incorporate into shiny module

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• need a filter on genetic distance long data frame that excludes rows in which it is self vs self

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation.

[jennahamlin]

remove rows with duplicated names in two columns (self compared to self)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label)%>%
  dplyr::distinct(label, value, .keep_all=T)   #Reduced the matrix to half of observations but still keeps rows in which the two ids are the same

geneFile4 <-geneFile3[which(geneFile3$label != geneFile3$name),]
#https://stackoverflow.com/questions/45720038/remove-rows-with-same-name-in-different-columns

[jennahamlin]

added exclude self vs self comparisons in snp_anno function

##read in genetic distance matrix
geneFile <-
  readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                    delim = "\t",
                    trim_ws = T, 
                    skip_empty_rows = T,
                    col_names = T)
#str(geneFile)

geneFile2 <- dplyr::rename(geneFile, label=1)%>%
  replace(., .=="-", 0)

#convert to long data frame - three columns
geneFile3 <- geneFile2%>%
  na.omit()%>%
  tidyr::pivot_longer(-label) 

geneFile4 <-geneFile3[which(geneFile3$label != geneFile3$name),]

# #https://stackoverflow.com/questions/45720038/remove-rows-with-same-name-in-different-columns

##read in tree file 
treeFile <-treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")

tree_plot <-
  ggtree::ggtree(treeFile) +
  ggtree::geom_tiplab() +
  ggplot2::xlim(NA, 0.02)

tree_plot

############### now to get it to work for more than one label 
tip_vector<-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"),c("2015C-3777_fastx5", "2015C-3506_fastx5"))

snpVector <- c()

snp_anno <- function(geneFile, tips){ 
  for (i in 1:length(tips)){
    for (j in 1:length(tips)){
      if(tips[i] == tips[j]) next #https://stackoverflow.com/questions/36329183/exclude-one-fixed-variable-in-for-loop
      snpVector[i]<- geneFile%>%
        dplyr::filter(label == tips[i] & name == tips[j]) %>%
        dplyr::pull(value)
          }
  }
  return(as.numeric(snpVector))
}

snpMean <-lapply(1:2, function(i)
  snp_anno(geneFile = geneFile4,
           tips= tip_vector[[i]]))

str(snpMean)

lapply(snpMean, mean)

make_layer <- function(tree, tips, label, color) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color
  )
}

#adjust lapply here to 1:2 when testing for two annotations with snp means
tree_plot + lapply(1:2, function(i)
  make_layer(
    tree_plot,
    tips = tip_vector[[i]],
    label = paste("Clade", "\n# SNPs -", lapply(snpMean[i], mean)),
    color = "red"
  ))

[jennahamlin]

Completed

• added an if statement to exclude self-comparisons for snp mean annotations

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation.
• Get snp annotation function incorporated into shiny module

[jennahamlin]

adding snp calculation to annotation

This works but can not get it to work in r shiny module

library(shiny)
library(treeio)
library(ggtree)
library(phytools)
library(ape)

##read in tree file 
treeFile <-treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")
tree_plot <-phytools::midpoint.root(treeFile)

##read in genetic distance matrix
dataFile <-readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",delim = "\t",trim_ws = T, skip_empty_rows = T,col_names = T)

# Define UI for application that draws a histogram
ui <- fluidPage(

  # Application title
  titlePanel("Test"),

  actionButton("add_annotation","Add clade annotation"),

  # Show a plot of the generated distribution
  mainPanel(
    plotOutput("treeDisplay", brush ="plot_brush"),
            plotOutput("treeDisplay2"),
            textOutput("contents")

  )
)

# Define server logic required to draw a histogram
server <- function(input, output) {

geneObject <- dplyr::rename(dataFile, label = 1)%>%  
      replace(., .=="-", 0) 

  geneFile <- 
    geneObject%>%
      na.omit()%>%
      tidyr::pivot_longer(-label)

  #remove self comparisons for this table - necessary for snp mean/median calculation. 
  geneFileSNP <-
    geneFile[which(geneFile$label != geneFile$name),]

  #reactive that holds base tree - this is how I am building the base tree
  make_tree <- reactive({
    ggtree::ggtree(tree_plot) +
      ggtree::geom_tiplab() +
      ggplot2::xlim(NA, 0.1)
  })

  #render base tree
  output$treeDisplay <- renderPlot({
    make_tree()
  })

  # Initialize a reactive value and set to zero
  n_annotations <- reactiveVal(0)
  annotations <- reactiveValues()

  #reactive that holds the brushed points on a plot
  dataWithSelection <- reactive({
    brushedPoints(make_tree()$data, input$plot_brush)
  })

  tipVector <- c()

  #add to label to vector if isTip == True
  dataWithSelection2 <- eventReactive(input$plot_brush, {
    for (i in 1:length(dataWithSelection()$label)) {
      if (dataWithSelection()$isTip[i] == TRUE)
        tipVector <- c(tipVector, dataWithSelection()$label[i])
    }
    return(tipVector)
  })

  snpVector <- c()

  snp_anno <- function(geneFile, tips){
    for (i in 1:length(tips)){
      for (j in 1:length(tips)){
        if(tips[i] == tips[j]) next #https://stackoverflow.com/questions/36329183/exclude-one-fixed-variable-in-for-loop
        snpVector[i]<- geneFile%>%
          dplyr::filter(label == tips[i] & name == tips[j]) %>%
          dplyr::pull(value)
      }
    }
    return(as.numeric(snpVector))
  }

  make_layer <- function(tree, tips, label, color) {
    ggtree::geom_cladelabel(
      node = phytools::findMRCA(ape::as.phylo(tree), tips),
      label = label,
      color = color,
      offset = 0.02
    )
  }

  snpMean <- eventReactive(input$add_annotation, {
    str(annotations[[paste0("ann", n_annotations())]] <- dataWithSelection2())

    lapply(1:n_annotations(), function(i)
      snp_anno(geneFile = geneFileSNP,
               tips = annotations[[paste0("ann", i)]]
      ))
  })

  #display that layer onto the tree
  anno_plot <- eventReactive(input$add_annotation, {
    # update the reactive value
    new <- n_annotations() + 1
    n_annotations(new)
    annotations[[paste0("ann", n_annotations())]] <- dataWithSelection2()

    plt <-
      make_tree() +
      lapply(1:n_annotations(), function(i)
        make_layer(
          make_tree(),
          tips = annotations[[paste0("ann", i)]],
          label = paste("Clade", "\nSNP -", lapply(snpMean()[i], mean)),
          color = "red"
        ))

    return(plt)
  })

  output$treeDisplay2 <- renderPlot({
    anno_plot()
  })

}

# Run the application 
shinyApp(ui = ui, server = server)

[jennahamlin]

Completed

• snp annotation function incorporated into shiny module and calculates mean for selected tips

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation - Is this possible?
• incorporate the use of the meta data file to get nice tip labels

[jennahamlin]

switch ugly/excess tip labels with pretty/labels in R

#load meta data which has key value pairs
metaFile <- readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_metaData.csv", delim = ",",trim_ws = T, skip_empty_rows = T,col_names = T  )

dataFile <-readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",delim = "\t",trim_ws = T, skip_empty_rows = T,col_names = T)

#https://stackoverflow.com/questions/11518958/replacing-columns-names-using-a-data-frame-in-r
#https://stackoverflow.com/questions/50007250/changing-column-names-except-for-the-first-two-columns
colnames(dataFile)[2:ncol(dataFile)] = metaFile$Display.labels[which(metaFile$Tip.labels %in% colnames(dataFile)[2:ncol(dataFile)])]
dataFile$. = metaFile$Display.labels[which(metaFile$Tip.labels %in% dataFile$.)]

[jennahamlin]

switch ugly/excess tip labels with pretty/labels in shiny

##read in genetic distance matrix
dataFile <-reactive({readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",delim = "\t",trim_ws = T, skip_empty_rows = T,col_names = T)})

metaFile <- reactive({readr::read_delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_metaData.csv", delim = ",",trim_ws = T, skip_empty_rows = T,col_names = T  )})

#numCols <-reactive(2:ncol(dataFie()))
dataFileCols <- reactive({
  dataFile2 <- dataFile()
  colnames(dataFile2)[2:ncol(dataFile2)]<-metaFile()$Display.labels[which(metaFile()$Tip.labels %in% colnames(dataFile2)[2:ncol(dataFile2)])]
  return(dataFile2)
})

dataFileRows <- reactive({
  dataFile3 <- dataFileCols()
  dataFile3$. = metaFile()$Display.labels[which(metaFile()$Tip.labels %in% dataFile3$.)]
  return(dataFile3)
})

[jennahamlin]

Completed

• can use meta data to change label in genetic distance matrix

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation - Is this possible?
• incorporate the use of the meta data file to get nice tip labels into module

[jennahamlin]

change tip labels in phylogenetic tree in R

#load tree and convert tibble - can access tip names by $label
treeFile <-treeio::read.newick("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1.dnd")

treeFile2 <- phylotools::sub.taxa.label(treeFile, as.data.frame(metaFile))

[jennahamlin]

read in tree file and if meta data file present incorporate as well - Shiny

library(shiny)

ui <- fluidPage(
  fileInput("treefile", label= "tree"),
  fileInput("metafile", "Choose CSV File",
            multiple = FALSE,
            accept = c("text/csv",
                       "text/comma-separated-values,text/plain",
                       ".csv")),
  actionButton("add_tree","Visualize Tree"),
  plotOutput("treeDisplay"),
  tableOutput("contents")
)

server <- function(input, output) {

  get_file_or_default <- reactive({ #this does tip label fix but doesn't work if a meta file is not uploaded
    if (is.null(input$metafile$datapath)) {
      treeio::read.newick(input$treefile$datapath)
    } else {

      dataFile <- readr::read_delim(input$metafile$datapath,
                        delim = ",",
                        trim_ws = T,
                        skip_empty_rows = T,
                        col_names = T)

    treeio::read.newick(input$treefile$datapath)%>%
      phylotools::sub.taxa.label(., as.data.frame(dataFile))
    }
  })

  #reactive that holds base tree - this is how I am building the base tree
  make_tree <- reactive({
    ggtree::ggtree(get_file_or_default()) +
      ggtree::geom_tiplab() +
      ggplot2::xlim(NA, 0.1)
  })

  #displays the tree plot, uses output from the displayTree module
  observeEvent(input$add_tree, {output$treeDisplay <- renderPlot({
    make_tree()})
  })

}

shinyApp(ui, server)

[jennahamlin]

Completed

• can upload optional meta data file to change tip labels in RShiny Module

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation - Is this possible?
• need to connect meta data file to genetic distance matrix in R shiny; this will allow the annotation function to work as is when tip labels change there is disconnect between tip labels and genetic distance matrix

[jennahamlin]

read in genetic distance data and if meta data present change tip labels in genetic distance

library(shiny)

ui <- fluidPage(

  fileInput("geneFile", "Choose gene File",
            multiple = FALSE,
            accept = c("text/csv",
                       "text/comma-separated-values,text/plain",
                       ".csv")),

  fileInput("metaFile", "Choose meta File",
            multiple = FALSE,
            accept = c("text/csv",
                       "text/comma-separated-values,text/plain",
                       ".csv")),

    tableOutput("contents")
)

server <- function(input, output) {

  get_file_or_default <- reactive({ 
    if (is.null(input$metaFile$datapath)) {

      geneFile2 <- readr::read_delim(input$geneFile$datapath,
                                    delim = "\t",
                                    trim_ws = T,
                                    skip_empty_rows = T,
                                    col_names = T)
       } 
      else {

        geneFile2 <- readr::read_delim(input$geneFile$datapath,
                                       delim = "\t",
                                       trim_ws = T,
                                       skip_empty_rows = T,
                                       col_names = T)

         metaFile2 <- readr::read_delim(input$metaFile$datapath,
                                       delim = ",",
                                       trim_ws = T,
                                       skip_empty_rows = T,
                                       col_names = T)

        colnames(geneFile2)[2:ncol(geneFile2)] = metaFile2$Display.labels[which(metaFile2$Tip.labels %in% colnames(geneFile2)[2:ncol(geneFile2)])]

        geneFile2$. = metaFile2$Display.labels[which(metaFile2$Tip.labels %in% geneFile2$.)]

        return(geneFile2)
        return(metaFile2)
      }
    })

   output$contents <- renderTable({
     get_file_or_default()
   })

}

shinyApp(ui, server)

[jennahamlin]

Completed

• connected meta data file to genetic distance matrix in R shiny - need to incorporate in module

Issues

• can I make the read in file a function so the code is not copied
• midpoint root is broken with meta data and tip labels.
• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• Optional meta data upload for tree and genetic distance incorporated into module and annotation

Issues

• can I make the read in file a function so the code is not copied
• midpoint root is broken with meta data and tip labels.
• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• made the read in file a function so the code is not copied

Issues

• midpoint root is broken with meta data and tip labels.
• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• midpoint root is reconnected

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• when uploading a new tree without closing the application, unable to add annotations to tree
• can remove annotations except for the first placed annotation. Similar problem mechanism for the statement above ("when uploading a new...")

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?
• need more informative error messages for when uploading files

[jennahamlin]

Completed

• added a reload function to start a new without having to close the application by the user

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• can remove annotations except for the first placed annotation.

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?
• need more informative error messages for when uploading files

[jennahamlin]

function to check if an annotation is present

offset <- function(make_treeOut){
    if (make_treeOut()$data$x == TRUE){
      max(make_treeOut()$data$x) + 0.02
    }
    else{
      max(make_treeOut()$data$x)
    }
  }

in theory, I want something to test if there is annotation on tree and if a new annotation overlaps, then move it over by X amount (here - 0.02)

[jennahamlin]

Completed

• added a check to make sure selected delimiter matches the file type that is uploaded for genetic distance and meta data files

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• can remove annotations except for the first placed annotation
• can we download files made on cdc server instance of tinsel? - at current unable

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• made file delimiter checking a function

Issues

• bootstrap displays values 1 - 9, need to convert these values to 01 - 09 to be ignored - have a local R option but unable to get working in R shiny
• can remove annotations except for the first placed annotation
• can we download files made on cdc server instance of tinsel? - at current unable

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• bootstrap displays values working properly from 0 - 100

Issues

• can remove annotations except for the first placed annotation
• can we download files made on cdc server instance of tinsel? - brought this up in meeting on 06/01 with scicomp
• need to do a check for annotations and if one is there then move over - important for overlapping annotations

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible?

[jennahamlin]

Completed

• cdc tinsel instance is now functional again :)

Issues

• can remove annotations except for the first placed annotation
• can we download files made on cdc server instance of tinsel? - brought this up in meeting on 06/01 with scicomp - need to file a new ticket (06/05)
• need to do a check for annotations and if one is there then move over - important for overlapping annotations
• what about mean SNPs that are less than 1 - need to convert that to 1?

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible? bookmarking

[jennahamlin]

Completed

• emailed biome team for user experience request on cdc server

Issues

• can remove annotations except for the first placed annotation
• can we download files made on cdc server instance of tinsel? - brought this up in meeting on 06/01 with scicomp - filed a new ticket (06/08)
• need to do a check for annotations and if one is there then move over - important for overlapping annotations
• what about mean SNPs that are less than 1 - need to convert that to 1?

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible? bookmarking

[jennahamlin]

Completed

• can step annotations back one by one; when two are on plot then plot will refresh and then only one annotation will be there when added rather than maintaining the first placed annotation from previous step back

Issues

• can we download files made on cdc server instance of tinsel? -Yes - they can be but need to code it differently - potential solution just not implemented yet.
• need to do a check for annotations and if one is there then move over - important for overlapping annotations
• what about mean SNPs that are less than 1 - need to convert that to 1?

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible? bookmarking
• specify which file with incorrect selection of delimitation.

User Comments

• Up/down arrows need to have more meaningful increment. ±1 skews the plot too much
• What is your tree layout? Should be a radio button
• Font for taxa? Should be radio button
• force tree format and font style sections to only allow users to select one layout at a time
• add a section with test data
• observe button to re viz tree when removing annotations gets down to two as this clears the tree

[jennahamlin]

Completed

• Doesn't remove tree when removing annotations at the point of two annotations to remove
• Converted to 0 sig digits for calculating mean
• Use of radio buttons for tree format and font style forces only one button to be selected.

Issues

• can we download files made on cdc server instance of tinsel? -Yes - they can be but need to code it differently - potential solution just not implemented yet.
• need to do a check for annotations and if one is there then move over - important for overlapping annotations

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible? bookmarking
• specify which file with incorrect selection of delimitation.

User Comments

• Up/down arrows need to have more meaningful increment. ±1 skews the plot too much
• add a section with test data

[jennahamlin]

Completed

• can use zip download option on local machine and download now can happen from cdc server

Issues

• code for download will need to be re-written to incorporate the input options
• need to do a check for annotations and if one is there then move over - important for overlapping annotations

To Do

• Module for counting the number of tree images downloaded - probably by having user put in their name or contact info - add google analytics to shiny app - need to check if this is possible on cdc network - emailed scicomp about this issue- they are supposed to be getting back to me
• Add an upload save session module for user that wants to come back to annotation - Is this possible? bookmarking I am thinking this is not possible because of cdc server.
• specify which file with incorrect selection of delimitation.

User Comments

• Up/down arrows need to have more meaningful increment. ±1 skews the plot too much
• add a section with test data