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JakeConway/Generate_UpSetR_plot_with_SNP_Heat_Map.R

Last active December 27, 2016 06:13
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Generate_UpSetR_plot_with_SNP_Heat_Map.R
myplot <- function(data, colour){
data <- data[which(data$color == colour), ]
plot_title <- as.character(unique(data$project))
data <- count(data["mutation"])
data$freq <- as.numeric(data$freq)
data$mutation <- as.character(data$mutation)
data <- data[which(nchar(data$mutation) == 3), ]
data <- data[order(data$mutation), ]
bases <- strsplit(data$mutation, ">")
original <- unlist(lapply(bases, function(x){x <- x[1]}))
mutation <- unlist(lapply(bases, function(x){x <- x[2]}))
data$original <- original
data$mutation <- mutation
if(length(data[which(data$original == "-"), ]$original)!=0){
data[which(data$original == "-"), ]$original <- "__"
}
if(length(data[which(data$mutation == "-"), ]$mutation)!= 0){
data[which(data$mutation == "-"), ]$mutation <- "__"
}
check <- c("__", "G", "C", "T", "A")
missing <- check[!check %in% data$mutation]
add <- c()
if(length(missing) != 0){
for(i in 1:length(missing)){
add[i] <- missing[i]
}
add_original <- rep("A", length(missing))
add_freq <- rep(NA, length(missing))
add_data <- data.frame(mutation = add, freq = add_freq, original = add_original)
data <- rbind(data, add_data)
}
add <- c()
add_freq <- c()
missing <- check[!check %in% data$original]
if(length(missing) != 0){
for(i in 1:length(missing)){
add[i] <- missing[i]
}
add_mutation <- rep("A", length(missing))
add_freq <- rep(NA, length(missing))
add_data <- data.frame(mutation = add_mutation, freq = add_freq, original = add)
data <- rbind(data, add_data)
data[which(is.na(data$freq)), ]$freq <- 0
}
maxvalue <- max(data$freq)
plot <- (ggplot(data, aes_string(x="mutation", y = "original")) + theme(panel.background = element_rect("white"),
axis.ticks = element_blank(),
plot.margin = unit(c(0,1.5,0.3,1.5), "cm"),
plot.title = element_text(color=colour, size = 10),
axis.title.x = element_text(size = 8.3),
axis.title.y = element_text(size = 8.3),
axis.text.x = element_text(size = 7),
axis.text.y = element_text(size = 7),
legend.key.size = unit(0.4, "cm"),
legend.text = element_text(size = 7),
legend.title = element_text(size = 8.3),
legend.key.height = unit(0.4, "cm"))
+ geom_tile(aes(fill = freq)) + scale_fill_gradient(low="grey86", high = "grey16", na.value = "white", limits = c(0, maxvalue))
+ ggtitle(plot_title))
}
upset(myData, nsets = 6,
sets.x.label = "Mutations", mainbar.y.label = "Shared Mutations", mb.ratio = c(0.5,0.5),
order.by = "freq", nintersects = 30,
queries = list(list(query = intersects, params = list("LUSC-US"), color = "#E69F00"),
list(query = intersects, params = list("LUSC-KR"), color = "#56B4E9"),
list(query = intersects, params = list("LAML-KR"), color = "#009E73"),
list(query = intersects, params = list("THCA-SA"), color = "#F0E442"),
list(query = intersects, params = list("LUSC-KR", "LAML-KR"), color = "#0072B2"),
list(query = intersects, params = list("THCA-US"), color = "#D55E00")),
attribute.plots = list(gridrows = 80,
plots = list(list(plot = myplot, x = "#E69F00", queries = T),
list(plot = myplot, x = "#56B4E9", queries = T),
list(plot = myplot, x = "#009E73", queries = T),
list(plot = myplot, x = "#F0E442", queries = T),
list(plot = myplot, x = "#0072B2", queries = T),
list(plot = myplot, x = "#D55E00", queries = T)), ncols = 3),
set.metadata = list(data = setdata,
plots = list(list(type="hist", column = "Donors", assign =15),
list(type="text", column = "Site", assign = 8))))
Raw
icgcData.txt
"id" "chromosome" "start" "end" "mutation" "project" "THCA-US" "THCA-SA" "LUSC-US" "LUSC-KR" "LUSC-CN" "LAML-KR"
"MU62030" "7" 140453136 140453136 "A>T" "THCA-US + THCA-SA" 1 1 0 0 0 0
"MU68272" "1" 115256529 115256529 "T>C" "THCA-US + LAML-KR" 1 0 0 0 0 1
"MU1292768" "11" 533874 533874 "T>C" "THCA-US + LUSC-US" 1 0 1 0 0 0
"MU55099" "1" 115256530 115256530 "G>T" "THCA-US + LAML-KR" 1 0 0 0 0 1
"MU599538" "4" 146059006 146059006 "G>A" "THCA-US" 1 0 0 0 0 0
"MU588560" "4" 146059041 146059041 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4591128" "19" 9090831 9090831 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4591301" "11" 281566 281566 "A>G" "THCA-US" 1 0 0 0 0 0
"MU1808134" "16" 56782202 56782202 "C>T" "THCA-US" 1 0 0 0 0 0
"MU1317988" "11" 533875 533875 "G>T" "THCA-US + LUSC-US" 1 0 1 0 0 0
"MU4588877" "22" 20079439 20079439 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4535466" "2" 131976198 131976198 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4586003" "1" 158725536 158725536 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4589215" "1" 155932417 155932417 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586854" "X" 20156731 20156731 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589694" "4" 52777312 52777312 "T>C" "THCA-US" 1 0 0 0 0 0
"MU3897619" "4" 3443797 3443797 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4591298" "22" 42610592 42610592 "G>A" "THCA-US" 1 0 0 0 0 0
"MU3897445" "11" 18505466 18505466 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4588490" "6" 20402610 20402610 "C>T" "THCA-US" 1 0 0 0 0 0
"MU596170" "3" 38591931 38591931 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4533657" "8" 12957624 12957624 "C>G" "THCA-US" 1 0 0 0 0 0
"MU10466" "14" 105246551 105246551 "C>T" "THCA-US + LUSC-US" 1 0 1 0 0 0
"MU4587025" "1" 3427403 3427403 "T>C" "THCA-US" 1 0 0 0 0 0
"MU3890022" "6" 29454710 29454710 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4591276" "17" 38552660 38552660 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4398999" "3" 113505224 113505224 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4586760" "9" 84530744 84530744 "T>C" "THCA-US" 1 0 0 0 0 0
"MU31038" "8" 144940615 144940615 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591339" "9" 129456049 129456051 "CAG>-" "THCA-US" 1 0 0 0 0 0
"MU4591458" "5" 40937653 40937653 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4588765" "5" 36985887 36985887 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4590188" "5" 38448474 38448474 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4590568" "5" 76331518 76331518 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4589718" "6" 118228990 118228992 "GCG>-" "THCA-US" 1 0 0 0 0 0
"MU4586598" "6" 108230223 108230223 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589852" "6" 51900420 51900420 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589922" "6" 51921515 51921515 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587445" "6" 21595266 21595266 "->GGC" "THCA-US" 1 0 0 0 0 0
"MU4586625" "6" 24358038 24358038 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589528" "5" 148624541 148624541 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591888" "5" 52097426 52097426 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4589395" "6" 128135044 128135044 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4587008" "6" 90365677 90365677 "C>T" "THCA-US" 1 0 0 0 0 0
"MU9234186" "6" 90368423 90368423 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590215" "6" 79707237 79707237 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4592088" "6" 80228599 80228599 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590328" "6" 97051492 97051492 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4591915" "7" 55479606 55479606 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591422" "7" 14378197 14378197 "->T" "THCA-US" 1 0 0 0 0 0
"MU4590842" "7" 73609165 73609165 "T>C" "THCA-US" 1 0 0 0 0 0
"MU1823484" "7" 5401259 5401259 "G>-" "THCA-US" 1 0 0 0 0 0
"MU4591078" "7" 66410130 66410130 "G>T" "THCA-US" 1 0 0 0 0 0
"MU1937761" "7" 20782555 20782555 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586745" "5" 176893800 176893800 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4588652" "7" 51092971 51092971 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589408" "7" 50514709 50514709 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586428" "7" 35280519 35280519 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588575" "8" 22428458 22428458 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4588842" "7" 121668634 121668634 "T>G" "THCA-US" 1 0 0 0 0 0
"MU4589282" "7" 117234990 117234990 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4587255" "7" 117368303 117368303 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4586632" "7" 151859891 151859891 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587508" "7" 157874039 157874039 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589345" "7" 140155658 140155658 "T>A" "THCA-US" 1 0 0 0 0 0
"MU4590715" "6" 7231938 7231938 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586738" "6" 7404673 7404673 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591352" "6" 33967792 33967792 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591528" "6" 33169616 33169616 "T>A" "THCA-US" 1 0 0 0 0 0
"MU4592122" "5" 175530270 175530270 "C>A" "THCA-US" 1 0 0 0 0 0
"MU4592052" "6" 31911265 31911265 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591225" "6" 31996293 31996293 "C>A" "THCA-US" 1 0 0 0 0 0
"MU4586125" "6" 31602045 31602045 "C>A" "THCA-US" 1 0 0 0 0 0
"MU4589352" "6" 31516041 31516041 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591162" "6" 37254821 37254821 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589775" "5" 167887657 167887657 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591768" "5" 178555009 178555009 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587692" "5" 179150714 179150714 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4588392" "8" 59058923 59058923 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591972" "8" 109215251 109215251 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591845" "8" 72946042 72946042 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4588892" "8" 74231385 74231385 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4587178" "6" 150290338 150290338 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586055" "6" 157521926 157521926 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590948" "6" 157527496 157527496 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590025" "6" 142409595 142409595 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588828" "6" 142468447 142468447 "C>A" "THCA-US" 1 0 0 0 0 0
"MU4586675" "6" 137147485 137147485 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588948" "6" 138583995 138583995 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591592" "6" 74073506 74073506 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590998" "6" 74171794 74171794 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587438" "6" 74228523 74228523 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4586808" "8" 24774945 24774945 "A>-" "THCA-US" 1 0 0 0 0 0
"MU4586978" "8" 38264955 38264955 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4591698" "8" 37690634 37690634 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587635" "8" 42977872 42977872 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4472728" "8" 42259489 42259489 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590385" "8" 38831929 38831929 "C>-" "THCA-US" 1 0 0 0 0 0
"MU95507" "5" 140237165 140237165 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591338" "5" 10390572 10390572 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591148" "5" 140038918 140038918 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4587705" "5" 1443103 1443103 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4590772" "7" 95822462 95822462 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590335" "7" 94058709 94058709 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587565" "7" 111474657 111474657 "T>-" "THCA-US" 1 0 0 0 0 0
"MU4590912" "7" 101847718 101847718 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588335" "20" 4768882 4768882 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591908" "20" 29976952 29976952 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587798" "20" 20506939 20506939 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4588272" "3" 72897455 72897455 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4591085" "4" 2306946 2306946 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4587832" "4" 20555525 20555525 "G>C" "THCA-US" 1 0 0 0 0 0
"MU821272" "21" 11098733 11098733 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589458" "20" 61512289 61512289 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4591028" "20" 62657293 62657293 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586358" "20" 62198473 62198473 "C>T" "THCA-US" 1 0 0 0 0 0
"MU9230850" "20" 62198499 62198499 "C>-" "THCA-US" 1 0 0 0 0 0
"MU4591662" "20" 61947922 61947922 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589802" "21" 31654786 31654786 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4587192" "20" 31600702 31600702 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4474755" "20" 34809819 34809819 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586168" "20" 49575532 49575532 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588715" "22" 42262982 42262982 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586048" "22" 50436654 50436654 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4588342" "3" 69088082 69088082 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4589592" "3" 112357200 112357200 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4591965" "3" 9101882 9101882 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587755" "3" 57282228 57282228 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4588688" "3" 57543396 57543396 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586118" "3" 119469814 119469814 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586252" "3" 120628502 120628502 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587515" "2" 204259430 204259430 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4589768" "2" 179629473 179629473 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588082" "2" 190439928 190439928 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4588378" "3" 181430265 181430265 "C>-" "THCA-US" 1 0 0 0 0 0
"MU4588075" "3" 182937644 182937644 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4585968" "3" 183518272 183518272 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587748" "3" 183655701 183655701 "C>A" "THCA-US" 1 0 0 0 0 0
"MU4587712" "3" 151475099 151475099 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587185" "3" 156421217 156421217 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590258" "3" 142037638 142037638 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4590018" "3" 130284243 130284243 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590525" "21" 46363721 46363721 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589972" "21" 41414505 41414505 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4586485" "21" 43547305 43547305 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587022" "22" 26695087 26695087 "A>C" "THCA-US" 1 0 0 0 0 0
"MU4591345" "22" 17472966 17472966 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589895" "22" 30812008 30812008 "C>T" "THCA-US" 1 0 0 0 0 0
"MU13622456" "22" 30890948 30890948 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4589042" "22" 29445437 29445437 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4585982" "22" 30642618 30642618 "G>-" "THCA-US" 1 0 0 0 0 0
"MU4586992" "3" 4824425 4824425 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4587642" "21" 44836663 44836663 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588498" "22" 22055423 22055423 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586295" "21" 47552224 47552224 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587382" "21" 43838718 43838718 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4588962" "4" 111539506 111539506 "A>T" "THCA-US" 1 0 0 0 0 0
"MU4586935" "4" 123664933 123664933 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4590955" "3" 31641886 31641886 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4587262" "3" 36873948 36873948 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4586512" "3" 51969488 51969488 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4589965" "3" 52019429 52019429 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4588532" "3" 50679702 50679702 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591388" "3" 52266070 52266070 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4587762" "3" 52393384 52393384 "C>-" "THCA-US" 1 0 0 0 0 0
"MU4589845" "3" 41280634 41280634 "A>G" "THCA-US" 1 0 0 0 0 0
"MU4587205" "3" 47890987 47890987 "G>T" "THCA-US" 1 0 0 0 0 0
"MU4591105" "3" 46484938 46484938 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588568" "3" 9965966 9965966 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587332" "16" 32192662 32192662 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4591612" "18" 48190438 48190438 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4591605" "19" 12430333 12430333 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4587248" "19" 12989328 12989328 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587572" "18" 63491897 63491897 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590688" "18" 55247321 55247321 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4590082" "19" 8962361 8962361 "C>-" "THCA-US" 1 0 0 0 0 0
"MU4587988" "19" 8987282 8987282 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586098" "19" 3282183 3282183 "G>C" "THCA-US" 1 0 0 0 0 0
"MU4588222" "19" 889754 889754 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4586315" "19" 4523617 4523617 "C>G" "THCA-US" 1 0 0 0 0 0
"MU4587488" "19" 5844400 5844400 "T>C" "THCA-US" 1 0 0 0 0 0
"MU4592002" "19" 3821446 3821446 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4588462" "19" 4157169 4157169 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590412" "15" 40308702 40308702 "G>A" "THCA-US" 1 0 0 0 0 0
"MU4590068" "15" 69561469 69561469 "C>T" "THCA-US" 1 0 0 0 0 0
"MU4587938" "15" 72190581 72190581 "A>T" "THCA-US" 1 0 0 0 0 0
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