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global.R
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#---------------------- LOAD LIBRARIES ----------------------#
# load basic libraries
library(shiny)
library(shinydashboard)
library(shinyBS)
library(readr)
library(rsvg)
library(shinyWidgets)
library(RColorBrewer)
# load Manning-related libraries
library(svgPanZoom)
# load ui-related libraries
library(colourpicker)
library(DT)
# load other network libraries
library(data.tree)
library(jsonlite)
#---------------------- SOURCE R FILES ----------------------#
source("R/colorby.R")
source("R/readinput.R")
source("R/writekinasetree.R")
source("R/legendfunctions.R")
source("R/map2color.R")
source("R/convertID.R")
source("R/makejson.R")
source("R/colors.R")
source("R/radiobuttonswithimages.R")
#---------------------- READ IN AND ORGANIZE DATA ----------------------#
# read RDS
orig_svginfo = readRDS("Data/kintree.RDS")
# if you need to up date the data frame read in the new info here
orig_svginfo$dataframe = data.frame(read_tsv("Data/coral_dataframe.tsv"))
# remove NAs from subfamilies
NAs = which(is.na(orig_svginfo$dataframe$kinase.subfamily))
orig_svginfo$dataframe$kinase.subfamily[NAs] = ""
# remove NAs from HGNCs
NAs = which(is.na(orig_svginfo$dataframe$id.HGNC))
orig_svginfo$dataframe$id.HGNC[NAs] = ""
# add correct header
# orig_svginfo$header = "<svg viewBox=\"50 -10 800 640\" preserveAspectRatio=\"xMidYMid meet\"\n
orig_svginfo$header = "<svg width=\"940\" height=\"940\"\n
xmlns=\"http://www.w3.org/2000/svg\"\n
xmlns:xlink=\"http://www.w3.org/1999/xlink\" >\n"
# <defs>\n <style type=\"text/css\">\n
# @import url('https://fonts.googleapis.com/css?family=Roboto:700');\n
# text {font-family: \"Roboto-Bold\";\n }\n </style>\n </defs>"
# intitialize title
orig_svginfo$title = ""
# initilize legend
orig_svginfo$legend = c()
# add node opacity
orig_svginfo$dataframe$node.opacity = 1
# add node order
orig_svginfo$dataframe$node.selected = -1
# make svginfo (leaving the original intact)
svginfo = orig_svginfo
# assign node and branch orders
svginfo$dataframe$nodeorder = 1:nrow(svginfo$dataframe)
svginfo$dataframe$branchorder = 1:nrow(svginfo$dataframe)
# get example RNA data
rna_data = paste(readLines("Data/RNAdata.txt"),collapse="\n")
rna_abs_data = paste(readLines("Data/RNAdata_pluripotent.txt"),collapse="\n")
#---------------------- DEFAULT COLORS ----------------------#
# Default tree branch color
BG_col1 = "#D3D3D3"
# Default selected color
Cor_col = "#FA6958"
# 2-color heatmap colors
HM2_low = "#1EA0F7"
HM2_hi = "#FACE1E"
# default heatmap colors
HM_low = "#1b8ed1"
HM_med = "#e0e0e0"
HM_hi = "#FA6958"
### Qualtative Palettes ###
qualitative_palette_choices <- c('<img src="images/Erika.png">' = 'Erika',
'<img src="images/Accent.png">' = 'Accent',
'<img src="images/Dark2.png">' = 'Dark2',
'<img src="images/Paired.png">' = 'Paired',
'<img src="images/Pastel1.png">' = 'Pastel1',
'<img src="images/Pastel2.png">' = 'Pastel2',
'<img src="images/Set1.png">' = 'Set1',
'<img src="images/Set2.png">' = 'Set2',
'<img src="images/Set3.png">' = 'Set3')
# my qualitative palettes
Erika = c("#FA6958","#3F9FFC","#FAD53F","#B0E6C2","#B348A1","#2CD1E0","#BEC956","#7C64FF","#C2374A","#70BD93","#FFBB99","#BA97F2")
Accent = brewer.pal(8,"Accent")
Dark2 = brewer.pal(8,"Dark2")
Paired = brewer.pal(12,"Paired")
Pastel1 = brewer.pal(9,"Pastel1")
Pastel2 = brewer.pal(8,"Pastel2")
Set1 = brewer.pal(9,"Set1")
Set2 = brewer.pal(8,"Set2")
Set3 = brewer.pal(12,"Set3")
qualpalettes = list(Erika,Accent,Dark2,Paired,Pastel1,Pastel2,Set1,Set2,Set3)
names(qualpalettes) = c("Erika","Accent","Dark2","Paired","Pastel1","Pastel2","Set1","Set2","Set3")
if (! dir.exists('www/images')) {
dir.create('www/images', showWarnings = F)
}
drawmypalettes("Erika",Erika,"www/images",boxes =5)
drawmypalettes("Accent",Accent,"www/images",boxes =5)
drawmypalettes("Dark2",Dark2,"www/images",boxes =5)
drawmypalettes("Paired",Paired,"www/images",boxes =5)
drawmypalettes("Pastel1",Pastel1,"www/images",boxes =5)
drawmypalettes("Pastel2",Pastel2,"www/images",boxes =5)
drawmypalettes("Set1",Set1,"www/images",boxes =5)
drawmypalettes("Set2",Set2,"www/images",boxes =5)
drawmypalettes("Set3",Set3,"www/images",boxes =5)
### Sequential Palettes ###
sequential_palette_choices <- c(
'<img src="images/Greys.png">' = 'Greys',
'<img src="images/Reds.png">' = 'Reds',
'<img src="images/Oranges.png">' = 'Oranges',
'<img src="images/Greens.png">' = 'Greens',
'<img src="images/Blues.png">' = 'Blues',
'<img src="images/Purples.png">' = 'Purples')
# my sequential palettes
Greys = brewer.pal(3,"Greys")
Reds = brewer.pal(3,"Reds")
Oranges = brewer.pal(3,"Oranges")
Greens = brewer.pal(3,"Greens")
Blues = brewer.pal(3,"Blues")
Purples = brewer.pal(3,"Purples")
seqpalettes = list(Greys,Reds,Oranges,Greens,Blues,Purples)
names(seqpalettes) = c("Greys","Reds","Oranges","Greens","Blues","Purples")
drawmypalettes("Greys",Greys,"www/images")
drawmypalettes("Reds",Reds,"www/images")
drawmypalettes("Oranges",Oranges,"www/images")
drawmypalettes("Greens",Greens,"www/images")
drawmypalettes("Blues",Blues,"www/images")
drawmypalettes("Purples",Purples,"www/images")
### Divergent Palettes ###
divergent_palette_choices <- c('<img src="images/Blue_Grey_Coral.png">' = 'Blue_Grey_Coral',
'<img src="images/Bro_Grey_Tur.png">' = 'Bro_Grey_Tur',
'<img src="images/Pink_Grey_Gre.png">' = 'Pink_Grey_Gre',
'<img src="images/Pur_Grey_Gre.png">' = 'Pur_Grey_Gre',
'<img src="images/Pur_Grey_Or.png">' = 'Pur_Grey_Or',
'<img src="images/Red_Grey_Gre.png">' = 'Red_Grey_Gre')
# my divergent palettes
Blue_Grey_Coral = c("#1B8ED1","#e5e5e5","#FA6958")
Bro_Grey_Tur = c("#A6611A","#e5e5e5", "#018571")
Pink_Grey_Gre = c("#D01C8B","#e5e5e5", "#4DAC26")
Pur_Grey_Gre = c("#7B3294","#e5e5e5", "#008837")
Pur_Grey_Or = c("#E66101","#e5e5e5", "#5E3C99")
Red_Grey_Gre = c("#CA0020","#e5e5e5", "#404040")
divpalettes = list(Blue_Grey_Coral,Bro_Grey_Tur,Pink_Grey_Gre,Pur_Grey_Gre,Pur_Grey_Or,Red_Grey_Gre)
names(divpalettes) = c("Blue_Grey_Coral","Bro_Grey_Tur","Pink_Grey_Gre","Pur_Grey_Gre","Pur_Grey_Or","Red_Grey_Gre")
drawmypalettes("Blue_Grey_Coral",Blue_Grey_Coral,"www/images")
drawmypalettes("Bro_Grey_Tur",Bro_Grey_Tur,"www/images")
drawmypalettes("Pink_Grey_Gre",Pink_Grey_Gre,"www/images")
drawmypalettes("Pur_Grey_Gre",Pur_Grey_Gre,"www/images")
drawmypalettes("Pur_Grey_Or",Pur_Grey_Or,"www/images")
drawmypalettes("Red_Grey_Gre",Red_Grey_Gre,"www/images")
# Default group color palette
defaultpalette = colorRampPalette( c(
"#FA6958",
"#3F9FFC",
"#FAD53F",
"#B0E6C2",
"#B348A1",
"#2CD1E0",
"#BEC956",
"#7C64FF",
"#C2374A",
"#70BD93",
"#FFBB99",
"#BA97F2"
))(12)
# # Default group color palette
# defaultpalette = colorRampPalette( brewer.pal(11,"Paired"))(11)
# pal_divs = row.names(brewer.pal.info[brewer.pal.info[,2]=="div",])
# pal_seqs = row.names(brewer.pal.info[brewer.pal.info[,2]=="seq",])
# pal_quals = row.names(brewer.pal.info[brewer.pal.info[,2]=="qual",])
CurrentInfoPage = "About"