#shiny::runApp("inst/scSVA",launch.browser =TRUE)
require(reticulate)
require(rhdf5)
require(Matrix)
require(ggplot2)
require(Cairo)
require(MASS)
library(RColorBrewer)
require(colorRamps)
require(dichromat)
require(viridis)
require(colourpicker)
require(shiny)
require(shinydashboard)
require(shinythemes)
require(shinyFiles)
require(scales)
require(sp)
require(extrafont)
require(plyr)
require(dplyr)
require(ggrepel)
require(plotly)
require(plot3D)
require(DT)
require(data.table)
require(tableHTML)
require(future)
require(future.apply)
require(shinyBS)
require(shinyjqui)
require(shinyAce)
require(gridExtra)
#require(magick)
#require(googleComputeEngineR)
suppressMessages(loadfonts())
if(Sys.info()["sysname"]=="Darwin" & file.exists("~/.bash_profile")){
reticulate::use_python(dirname(system("source ~/.bash_profile; which python3",intern = T)))
} else if(Sys.info()["sysname"]=="Linux"){
reticulate::use_python(dirname(system("which python3",intern = T)))
}
if(file.exists("/.dockerenv")){Sys.setenv(PATH = paste("/opt/conda/bin/", Sys.getenv("PATH"),sep=":"))}
if(Sys.getenv("GOOGLE_CLOUD_SDK") == ""){
GCU<-if(Sys.info()["sysname"]=="Darwin" & file.exists("~/.bash_profile")){
system("source ~/.bash_profile; which gsutil",intern = T)
} else if(Sys.info()["sysname"]=="Linux"){
system("which gsutil",intern = T)
}
} else {
GCU<-file.path(Sys.getenv("GOOGLE_CLOUD_SDK"),"gsutil")
}
options(future.globals.maxSize=Inf)
plan(multiprocess)
options(warn=-1)
options(shiny.usecairo=FALSE)
numpy <- NULL
vaex <- NULL
gc_python <- NULL
vaex <-reticulate::import("vaex", convert = FALSE)
numpy <-reticulate::import("numpy", convert = FALSE)
gc_python <-reticulate::import("gc", convert = FALSE)
InitPlot<-read.table(gzfile(paste0(system.file("scSVA",package="scSVA"),"/scSVA.txt.gz")),
header = T,
sep = ",")
ds <- vaex$from_arrays(x = numpy$array(InitPlot$X),
y = numpy$array(InitPlot$Y),
Gene = numpy$array(InitPlot$Gene),
clusters = numpy$array(InitPlot$Cluster))
termOut <- NULL
vm <- NULL
tag <- NULL
Parameters.FA_3D <- NULL
FLE_dist <- NULL
Parameters.DMap <- NULL
Parameters.NNG <- NULL
modes <- getAceModes()
themes <- getAceThemes()
tmpdir<-tempdir()
#https://en.wikipedia.org/wiki/List_of_Crayola_crayon_colors
list.colors<-list(
Crayola.12 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A"),
Crayola.24 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A",
"#03BB85","#FFDF00","#8B8680","#0A6B0D","#8FD8D8","#A36F40","#F653A6","#CA3435","#FFCBA4","#FF99CC","#FA9D5A","#FFAE42"),
Crayola.36 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A",
"#03BB85","#FFDF00","#8B8680","#0A6B0D","#8FD8D8","#A36F40","#F653A6","#CA3435","#FFCBA4","#FF99CC","#FA9D5A","#FFAE42",
"#A78B00","#788193","#514E49","#1164B4","#F4FA9F","#FED8B1","#C32148","#01796F","#E90067","#FF91A4","#404E5A","#6CDAE7"),
Crayola.50 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A",
"#03BB85","#FFDF00","#8B8680","#0A6B0D","#8FD8D8","#A36F40","#F653A6","#CA3435","#FFCBA4","#FF99CC","#FA9D5A","#FFAE42",
"#A78B00","#788193","#514E49","#1164B4","#F4FA9F","#FED8B1","#C32148","#01796F","#E90067","#FF91A4","#404E5A","#6CDAE7",
"#FFC1CC","#006A93","#867200","#E2B631","#6EEB6E","#FFC800","#CC99BA","#00003B","#BC6CAC","#DCCCD7","#EBE1C2","#A6AAAE",
"#B99685","#0086A7"),
Crayola.60 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A",
"#03BB85","#FFDF00","#8B8680","#0A6B0D","#8FD8D8","#A36F40","#F653A6","#CA3435","#FFCBA4","#FF99CC","#FA9D5A","#FFAE42",
"#A78B00","#788193","#514E49","#1164B4","#F4FA9F","#FED8B1","#C32148","#01796F","#E90067","#FF91A4","#404E5A","#6CDAE7",
"#FFC1CC","#006A93","#867200","#E2B631","#6EEB6E","#FFC800","#CC99BA","#00003B","#BC6CAC","#DCCCD7","#EBE1C2","#A6AAAE",
"#B99685","#0086A7","#5E4330","#C8A2C8","#708EB3","#BC8777","#B2592D","#497E48","#6A2963","#E6335F","#03228E","#B5A895"),
Crayola.105 = c("#000000","#0066FF","#AF593E","#01A368","#FF861F","#ED0A3F","#FF3F34","#76D7EA","#8359A3","#FFFFFF","#FBE870","#C5E17A",
"#03BB85","#FFDF00","#8B8680","#0A6B0D","#8FD8D8","#A36F40","#F653A6","#CA3435","#FFCBA4","#FF99CC","#FA9D5A","#FFAE42",
"#A78B00","#788193","#514E49","#1164B4","#F4FA9F","#FED8B1","#C32148","#01796F","#E90067","#FF91A4","#404E5A","#6CDAE7",
"#FFC1CC","#006A93","#867200","#E2B631","#6EEB6E","#FFC800","#CC99BA","#00003B","#BC6CAC","#DCCCD7","#EBE1C2","#A6AAAE",
"#B99685","#0086A7","#5E4330","#C8A2C8","#708EB3","#BC8777","#B2592D","#497E48","#6A2963","#E6335F","#03228E","#B5A895",
"#0048ba","#EED9C4","#C88A65","#FDD5B1","#D0FF14","#B2BEB5","#926F5B","#00B9FB","#6456B7","#DB5079",
"#C62D42","#FA9C44","#DA8A67","#FD7C6E","#93CCEA","#FCF686","#503E32","#63B76C","#FF5470","#87421F",
"#9DE093","#FF7A00","#4F69C6","#A50B5E","#F0E68C","#FDFF00","#F091A9","#FF6E4A","#2D383A","#6F9940",
"#FC74FD","#652DC1","#D6AEDD","#EE34D2","#BB3385","#6B3FA0","#33CC99","#FFDB00","#87FF2A","#FC80A5",
"#D9D6CF","#00755E","#FFFF66","#7A89B8","#FF007C"),
Crayola_Mix = c("#000000","#95918C","#FDD9B5","#1F75FE","#FFAE42","#FFAACC","#1CAC78","#1DACD6","#7366BD","#FC2847",
"#50BFE6","#00468C","#C3CDE6","#0066FF","#91E351","#C0E7F1","#6ADA8E","#FFF7CC","#FFB97B","#FDFF00",
"#0048BA","#D0C6C6","#6E7FE7","#FF7A00","#6D3834","#0D98BA","#E7C697","#FF355E","#54626F","#66FF66",
"#AAF0D1","#FF00CC","#FFCC33"),
Crayola_Fluorescent = c("#FF355E","#FD5B78","#FF6037","#FF9966","#FF9933","#FFCC33","#FFFF66","#CCFF00","#66FF66","#AAF0D1","#50BFE6","#FF6EFF","#EE34D2","#FF00CC"),
Crayola_Silver_Swirls = c("#C39953","#AD6F69","#6EAEA1","#B768A2","#9E5E6F","#5F8A8B","#A17A74","#2E2D88","#AE98AA","#8BA8B7","#DA2C43","#914E75",
"#6D9BC3","#AB92B3","#BBB477","#5DA493","#778BA5","#8A496B","#CD607E","#676767","#AD4379","#A6A6A6","#5FA778","#56887D"),
Crayola_Magic_Scent = c("#FFFFFF","#CA3435","#FBE870","#8359A3","#000000","#0066FF","#ED0A3F","#FED85D","#C32148","#9E5B40","#FF8833","#C9A0DC",
"#FFA6C9","#FF3399","#4570E6","#AF593E","#29AB87","#C5E17A","#FFCBA4","#8B8680","#FC80A5","#76D7EA","#FDD5B1","#01786F","#C3CDE6"),
Crayola_Changeables = c("#C0E7F1","#91E351","#FF8071","#FF8ABA","#F4405D","#FDFD07","#EB58DD","#963D7F","#000000","#FFF7CC","#131391","#4F7948","#FFE9D1"),
Crayola_Pearl_Brite = c("#5FBED7","#E8F48C","#4F42B5","#F1444A","#54626F","#F37A48","#48BF91","#F2F27A","#6ADA8E","#702670","#7B4259","#F1CC79","#F5F5F5",
"#D65282","#F03865","#3BBCD0"),
Crayola_Glitter = c("#000000","#0D98BA","#1CAC78","#FF7538","#EE204D","#7851A9","#FFFFFF","#FCE883","#1F75FE","#FFAACC","#C8385A","#E6A8D7","#C0448F",
"#80DAEB","#C5E384"),
Crayola_Metallic_FX = c("#C46210","#2E5894","#9C2542","#BF4F51","#A57164","#58427C","#4A646C","#85754E","#319177","#0A7E8C","#9C7C38","#8D4E85","#8FD400",
"#D98695","#757575","#0081AB"),
Crayola_Gel_FX = c("#FFBF7F","#00D0B5","#7853A8","#63A5C3","#0081FF","#FF3399","#CF0060","#FFFFFF","#FF6699","#8F5873","#F26D7D","#6666CC","#F58345","#FFFF66",
"#99FF99","#12E3DB"),
Crayola_Silly_Scents = c("#C5E17A","#FED85D","#FF681F","#00CCCC","#D99A6C","#B94E48","#6456B7","#FF8833","#ECEBBD","#ED0A3F","#FC80A5","#E77200",
"#C32148","#8B8680","#F7468A","#76D7EA"),
Crayola_Heads_n_Tails = c("#FF3855","#FFAA1D","#2243B6","#A83731","#FD3A4A","#FFF700","#5DADEC","#AF6E4D","#FB4D46","#299617","#5946B2","#1B1B1B","#FA5B3D",
"#A7F432","#9C51B6","#BFAFB2"),
Crayola_Mini_Twistables= c("#FDD9B5","#000000","#1F75FE","#0D98BA","#7366BD","#B4674D","#FFAACC","#1DACD6","#FDDB6D","#95918C","#1CAC78","#F0E891","#5D76CB",
"#FF7538","#EE204D","#FF5349","#C0448F","#FC2847","#926EAE","#F75394","#FFFFFF","#FCE883","#C5E384","#FFAE42")
)
tmp <- dichromat::colorschemes
names(tmp) <- paste0("dichromat::",names(dichromat::colorschemes))
tmp.2 <- lapply(1:nrow(brewer.pal.info), function(x) brewer.pal(name=rownames(brewer.pal.info)[x],n=brewer.pal.info$maxcolors[x]))
names(tmp.2) <- rownames(brewer.pal.info)
list.colors <- c(list.colors,tmp,tmp.2)
dens_cols <- c("inferno", "viridis", "magma", "rainbow","matlab.like","matlab.like2","matlab.like3","gray.red",names(tmp),names(tmp.2))
rm(tmp,tmp.2)
gray.red <- function(n.colors){colorRampPalette(c("grey80","gray70","gray60","red","red2","red4","black"))(n.colors)}
matlab.like3 <- function(n.colors){c("black","gray20",matlab.like2(n.colors-2))}
get_colors <- function(palette,if.dichromat,d.type,n.colors){
if(!is.null(tryCatch(get(palette), error = function(e) {}))){
if(if.dichromat) {dichromat(do.call(palette,list(n.colors)),d.type)} else
{do.call(palette,list(n.colors))}
} else {
if(if.dichromat) {dichromat(colorRampPalette(list.colors[[palette]])(n.colors),d.type)} else
{colorRampPalette(list.colors[[palette]])(n.colors)}
}
}
plot_palette <- function(list.cols,
border = "gray80"){
plot(0, 0,
axes = FALSE,
xlab = "",
ylab = "",
xlim = c(0L, 1L),
ylim = c(0L, 1L),
type = "n")
N = length(list.cols)
rect(0:(N-1)/N, 0, 1:N/N, 1.0,
col = list.cols,
border = border)
}
#Violin plots
StatChull <- ggproto("StatChull", Stat,
compute_group = function(data, scales) {
tmp<-rbind(data.frame(x=data$y,y=data$x),
data.frame(x=-rev(data$y),y=rev(data$x)))
# tmp<-rbind(data.frame(x=tmp$x,y=tmp$y,col=rep(0,length(tmp$x))),
# data.frame(x=tmp$x,y=tmp$y,col=rep(1,length(tmp$x))),
# )
# tmp$col=factor(tmp$col)
tmp
},
default_aes = aes(weight = 1, colour = "grey20", fill = "white", size = 0.5,
alpha = NA, linetype = "solid"),
required_aes = c("x", "y")
)
stat_chull <- function(mapping = NULL, data = NULL, geom = "polygon",
position = "identity", na.rm = FALSE, show.legend = NA,
inherit.aes = TRUE, ...) {
layer(
stat = StatChull, data = data, mapping = mapping, geom = geom,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(na.rm = na.rm, ...)
)
}
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