Ranking according to value across two variables - r - r

I have this dataframe:
df<-data.frame(
var1 = c(rep(c(rep(1,2), rep(2,3), rep(3,2), rep(4,1)),2), 1),
var2 = c(rep(1,8), rep(2,8),3)
)
df
var1 var2
#1 1 1
#2 1 1
#3 2 1
#4 2 1
#5 2 1
#6 3 1
#7 3 1
#8 4 1
#9 1 2
#10 1 2
#11 2 2
#12 2 2
#13 2 2
#14 3 2
#15 3 2
#16 4 2
#17 1 3
I would like to make a third variable that is a rank. Rows get the highest rank if 1) they have the lowest numbers in var2 - and then according to how low the numbers are in var1. e.g. Rows 1 and 2 with var2=1 and var1=1 should be ranked 1. Whereas, rows 9 and 10 with var2=2 and var1=1 would be ranked 5.
If my data are arranged in ascending order of var2 and then var1, I did the following using my favorite R function rle to achieve the ranking I'm after:
rle(df$var1)
N <- length(rle(df$var1)$lengths)
df$ranks <- rep(1:N, rle(df$var1)$lengths)
df
var1 var2 ranks
#1 1 1 1
#2 1 1 1
#3 2 1 2
#4 2 1 2
#5 2 1 2
#6 3 1 3
#7 3 1 3
#8 4 1 4
#9 1 2 5
#10 1 2 5
#11 2 2 6
#12 2 2 6
#13 2 2 6
#14 3 2 7
#15 3 2 7
#16 4 2 8
#17 1 3 9
This works, but it requires my df to be pre-sorted. I'd like a solution that does not need this. I feel like this should be a simple one-liner using rank and that I'm having a blind-spot. Any help appreciated - thanks.
EDIT 1:
- adding a larger example for testing of suggested answer
dput(df1)
df1 <- structure(list(var1 = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 7L,
7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 6L, 9L, 10L, 10L, 10L, 11L,
12L, 12L, 12L, 13L, 14L, 14L, 14L, 14L, 15L, 16L, 16L, 16L, 16L,
16L, 17L, 17L, 17L, 17L, 17L, 18L, 18L, 18L, 18L, 18L, 19L, 19L,
20L, 20L, 21L, 22L, 22L, 22L, 22L, 22L, 23L, 23L, 23L, 23L, 23L,
24L, 24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 25L, 1L, 2L, 2L,
2L, 2L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L,
8L, 9L, 10L, 10L, 10L, 10L, 3L, 11L, 11L, 11L, 11L, 12L, 13L,
13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L,
12L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 17L, 18L, 18L, 18L,
18L, 18L, 19L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 21L, 22L,
22L, 22L, 23L, 25L, 24L, 24L, 24L, 24L, 24L, 26L, 26L, 26L, 26L,
26L, 27L, 27L, 27L, 27L, 27L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L,
6L, 7L, 7L, 7L, 7L, 7L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L,
11L, 12L, 12L, 13L, 14L, 15L, 16L, 17L, 17L, 18L, 18L, 19L, 19L,
19L, 19L, 20L, 21L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 22L,
23L, 23L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 24L, 25L, 25L, 25L,
25L, 25L, 26L, 26L, 26L, 27L, 27L, 28L, 28L, 28L, 28L, 28L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 4L, 4L,
4L, 4L, 5L, 6L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L), var2 = c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), ranks = c(1L, 1L,
1L, 1L, 1L, 12L, 12L, 12L, 12L, 12L, 19L, 19L, 19L, 19L, 19L,
20L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 21L, 23L, 23L, 23L,
23L, 23L, 24L, 24L, 24L, 24L, 24L, 22L, 25L, 2L, 2L, 2L, 3L,
4L, 4L, 4L, 5L, 6L, 6L, 6L, 6L, 7L, 8L, 8L, 8L, 8L, 8L, 9L, 9L,
9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 13L, 13L, 14L,
15L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 16L, 17L, 17L, 17L,
17L, 17L, 18L, 18L, 18L, 18L, 18L, 26L, 37L, 37L, 37L, 37L, 47L,
48L, 48L, 48L, 48L, 49L, 49L, 49L, 49L, 49L, 50L, 50L, 50L, 50L,
51L, 52L, 27L, 27L, 27L, 27L, 46L, 28L, 28L, 28L, 28L, 29L, 30L,
30L, 30L, 30L, 31L, 31L, 31L, 31L, 31L, 32L, 32L, 32L, 32L, 32L,
29L, 33L, 33L, 33L, 33L, 34L, 34L, 34L, 34L, 34L, 35L, 35L, 35L,
35L, 35L, 36L, 36L, 36L, 36L, 36L, 38L, 38L, 38L, 38L, 39L, 40L,
40L, 40L, 41L, 43L, 42L, 42L, 42L, 42L, 42L, 44L, 44L, 44L, 44L,
44L, 45L, 45L, 45L, 45L, 45L, 53L, 64L, 64L, 64L, 64L, 74L, 74L,
74L, 74L, 74L, 75L, 75L, 75L, 75L, 75L, 76L, 76L, 76L, 76L, 76L,
77L, 77L, 77L, 77L, 77L, 78L, 78L, 78L, 78L, 78L, 79L, 80L, 80L,
80L, 80L, 54L, 54L, 54L, 54L, 55L, 56L, 56L, 57L, 58L, 59L, 60L,
61L, 61L, 62L, 62L, 63L, 63L, 63L, 63L, 65L, 66L, 66L, 66L, 66L,
66L, 67L, 67L, 67L, 67L, 67L, 68L, 68L, 68L, 68L, 68L, 69L, 69L,
69L, 69L, 69L, 70L, 70L, 70L, 70L, 70L, 71L, 71L, 71L, 72L, 72L,
73L, 73L, 73L, 73L, 73L, 81L, 81L, 81L, 81L, 81L, 82L, 82L, 82L,
82L, 82L, 83L, 83L, 83L, 83L, 83L, 84L, 84L, 84L, 84L, 85L, 86L,
87L, 87L, 87L, 87L, 88L, 88L, 88L, 88L, 88L)), .Names = c("var1",
"var2", "ranks"), row.names = c(NA, -300L), class = "data.frame")
The ranks variable was got from this suggested answer:
df1$ranks1 <- dense_rank(paste(df1$var2, df1$var1))

Solutions involving paste[0] will only work if values within each vector are integer with a fixed number of digits. This is because paste converts to character and:
character (lexicographic) ordering differs from numeric: rank(c(1 , 2, 11)); rank(as.character(c(1 , 2, 11)))
concatenation introduces ambiguities: paste0(2,12); paste0(21,2)
Peter Dalgaard made a relevant post in 2011 http://r.789695.n4.nabble.com/Function-rank-for-data-frames-or-multiple-vectors-td3765685.html
For now ignore identical rows. Note that rank(x) == order(order(x)) and order accepts multiple ordering columns so if you don't mind how identical rows are split order(order(df$var2, df$var1)) does the job.
This splits identical rows according to their original ordering. There are a number of ways of ranking identical rows http://en.wikipedia.org/wiki/Ranking#Strategies_for_assigning_rankings.
In 2011 Peter Dalgaard suggested ave(order(order(df$var2, df$var1)), df$var2, df$var1) which gives what Wikipedia calls 'Fractional ranking' and in base::rank is the default ties.method="average".
Your example is what Wikipedia calls 'Dense ranking' which isn't available in base::rank but - as commented by David Arenburg - is provided by dplyr::dense_rank, so you can library(dyplr) and use:
dense_rank(ave(order(order(df$var2, df$var1)), df$var2, df$var1))
Looking at the code for dense_rank it is just
function (x)
{
r <- rank(x)
match(r, sort(unique(r)))
}
suggesting that if you don't want to load dplyr and are happy with a 2-statement solution creating another variable - e.g. r - you could use
r <- ave(order(order(df$var2, df$var1)), df$var2, df$var1); match(r, sort(unique(r)))
Edited to add ...
You can make things a little neater by realising that a data frame is really a list so to rank by columns in order of occurrence:
dense_rank(ave(order(do.call(order, df)), df))
You are ranking by columns in reverse order of occurrence so
dense_rank(ave(order(do.call(order, rev(df))), df))
or explicitly specifying columns and their order
dense_rank(ave(order(do.call(order, df[,2:1])), df[,2:1]))

Related

R plotly multiple plots only show last figure

I would like to make an interactive graphs based on user input. However I'm struggle to make more than one graphs using R plotly. Suppose I have following data and codes,
dput(norwd5)
structure(list(LENGTH_OF_STAY = c(57L, 28L, 15L, 28L, 14L, 49L,
15L, 22L, 17L, 81L, 34L, 24L, 31L, 38L, 33L, 22L, 21L, 49L, 188L,
21L, 21L, 36L, 24L, 23L, 48L, 54L, 42L, 62L, 13L, 139L, 29L,
49L, 15L, 7L, 43L, 28L, 31L, 22L, 23L, 26L, 33L, 30L, 127L, 22L,
22L, 15L, 28L, 26L, 15L, 31L, 22L, 89L, 28L, 60L, 54L, 37L, 20L,
135L, 155L, 51L, 15L, 8L, 38L, 16L, 16L, 22L, 30L, 14L, 16L,
18L, 14L, 272L, 25L, 22L, 18L, 21L, 188L, 264L, 34L, 34L, 136L,
23L, 142L, 25L, 32L, 58L, 163L, 16L, 35L, 23L, 50L, 71L, 10L,
19L, 22L, 24L, 45L, 29L, 15L, 82L), PRE_OPERATIVE_LOS = c(2L,
2L, 3L, 1L, 3L, 6L, 3L, 7L, 2L, 2L, 11L, 2L, 6L, 3L, 6L, 3L,
5L, 3L, 179L, 2L, 5L, 3L, 4L, 2L, 5L, 6L, 2L, 4L, 2L, 6L, 3L,
2L, 2L, 6L, 6L, 1L, 4L, 5L, 6L, 5L, 0L, 4L, 6L, 2L, 4L, 4L, 7L,
4L, 4L, 6L, 2L, 4L, 3L, 3L, 2L, 6L, 4L, 110L, 63L, 6L, 4L, 7L,
5L, 1L, 6L, 1L, 4L, 2L, 6L, 3L, 2L, 8L, 2L, 2L, 4L, 3L, 6L, 171L,
5L, 4L, 116L, 6L, 47L, 3L, 7L, 3L, 60L, 1L, 3L, 20L, 31L, 49L,
9L, 8L, 3L, 4L, 35L, 7L, 4L, 9L), POST_OPERATIVE_LOS = c(55L,
26L, 12L, 27L, 11L, 43L, 12L, 15L, 15L, 79L, 23L, 22L, 25L, 35L,
27L, 19L, 16L, 46L, 9L, 19L, 16L, 33L, 20L, 21L, 43L, 48L, 40L,
58L, 11L, 133L, 26L, 47L, 13L, 1L, 37L, 27L, 27L, 17L, 17L, 21L,
33L, 26L, 121L, 20L, 18L, 11L, 21L, 22L, 11L, 25L, 20L, 85L,
25L, 57L, 52L, 31L, 16L, 25L, 92L, 45L, 11L, 1L, 33L, 15L, 10L,
21L, 26L, 12L, 10L, 15L, 12L, 264L, 23L, 20L, 14L, 18L, 182L,
93L, 29L, 30L, 20L, 17L, 95L, 22L, 25L, 55L, 103L, 15L, 32L,
3L, 19L, 22L, 1L, 11L, 19L, 20L, 10L, 22L, 11L, 73L), digoxin_any = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
2L, 1L, 2L), .Label = c("0:No", "1.Yes"), class = "factor")), row.names = c(NA,
-100L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x0000012f36b61ef0>)
num <- c('PRE_OPERATIVE_LOS','POST_OPERATIVE_LOS')
plist <- scan(text=num,what = "",quiet = T)
groups <- 'digoxin_any'
bygrp <- scan(text=groups,what="",quiet=T)
norwd5[, (bygrp) := lapply(.SD, as.factor), .SDcols = bygrp]
plotList = list()
for(i in length(plist)){
gplot <- ggplot(norwd5,aes_string(x=plist[i],group=bygrp,color=bygrp))+geom_histogram(aes(y=..density..),position = "dodge")+geom_density(alpha=.5) +theme(legend.position = "left")
plotList[[i]] <- plotly_build(gplot)
}
for(i in length(plist)){
print(plotList[[i]])
}
The goal is to show both graphs for PRE_OPERATIVE_LOS and POST_OPERATIVE_LOS. However, the codes above only show histogram for POST_OPERATIVE_LOS.
I checked maybe subplot is the way to go but how to make subplot work in a loop? Any hints?
Thanks!
There is an error in your first loop and calling each subplot won't make both appear at the same time.
First-- the issue with your first for call- when you wrote
for(i in length(plist))
You wrote for i in 2 or i == 2, meaning that you never looped. If you modify it to a range of values, now it's written: for i in 1 to 2.
for(i in 1:length(plist))
So you're aware, if you had written for(i in plist) it would have done both loops, but instead of a value, i would be the strings.
Okay, so now there are two graphs. From the plotly library, you can use the function subplot. You will want to turn the legend off for one of them, though.
subplot(plotList[[1]],
style(plotList[[2]], showlegend = FALSE))
If you wanted the outline color, that's more than okay! However, if you wanted to bars to be filled, you need to assign fill instead of color.
If you change color = bygrp to fill = bygrp, this is how this would change:
If you leave the color assignment and add fill = bygrp (so you have both), this is how this would change:

R loess regression

I think I missed something in the use of the loess function and I can't understand what i did wrong. I have a data frame in which I store the output (count) of 3 different softwares for 26 different genes on the genomes of different patients. The 3 softwares were each used on the same genome but with different rate of downsampling.
I pooled the results of all the patients by genes. At the end I have a data frame with 4 columns: samplexxx (downsampling rate), software (name of the software I used), gene (the name of the gene) and count (count results given by the software).
My goal is to estimate the downsampling effect (samplexxx) on the count given by the software, and I want to do some regression to be able to compare them with each other.
rate <- c(5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,
95, 100)
my attempts:
datalist <- list()
for (i in 1:22) {
name <- genes[i]
print(name)
mod <- paste("mod_", name)
xfit <- paste("xfit_", name)
df <- paste("df_", name)
mod <- loess(data2[data2$gene == name,]$count ~
data2[data2$gene == name,]$samplexxx)
xfit <- predict(mod, newdata=data2[data2$gene == name,]$samplexxx)
df <- setNames(data.frame(matrix(ncol=4, nrow=60)),
c("down", "software", "gene", "loess"))
df$down <- data2[data2$gene == name,]$samplexxx
df$software <- data2[data2$gene == name,]$software
df$gene <- data2[data2$gene == name,]$gene
df$loess <- xfit
print(xfit)
datalist[[i]] <- df
}
data_loess <- do.call(rbind, datalist)
ggplot(data_loess, aes(x=gene, y=loess, fill=software)) +
geom_boxplot()
and:
mod <- loess(data2$count ~ data$samplexxx)
xfit <- predict(mod, newdata=data2$samplexxx)
for (i in 1:20) {
down <- rate[i]
print(name)
title <- paste("loess_downsampling", down)
out <- paste("loess_downsampling", down, ".pdf", sep="")
pdf(out, width=10)
print(ggplot(data2, aes(x=down, y=loess, fill=software))) +
geom_boxplot() + ggtitle(title))
dev.off()
}
Sample data:
> dput(data2)
structure(list(samplexxx = c(5L, 10L, 15L, 20L, 25L, 30L, 35L,
40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L,
45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L,
5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L,
70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L,
35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L,
100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L,
65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L,
30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L,
95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,
60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L,
25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L,
90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L,
55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L, 15L,
20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L,
85L, 90L, 95L, 100L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L,
50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 5L, 10L,
15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L,
80L, 85L, 90L, 95L, 100L), software = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L), .Label = c("EH", "GangSTR", "Tred"), class = "factor"),
gene = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L,
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L,
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 18L, 18L, 18L, 18L,
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L,
18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L,
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L,
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L,
19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L,
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L,
13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L,
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L), .Label = c("AFF2", "AR", "ATN1", "ATXN1",
"ATXN10", "ATXN2", "ATXN3", "ATXN7", "C9ORF72", "CACNA1A",
"CBL", "CNBP", "CSTB", "DIP2B", "DMPK", "FMR1", "FXN", "HTT",
"JPH3", "NOP56", "PPP2R2B", "TBP"), class = "factor"), count = c(NA,
NA, NA, NA, NA, NA, NA, NA, NA, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, NA, NA, NA, NA, NA, NA, NA,
NA, NA, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, NA, NA, NA, NA, NA, NA, NA, NA, NA, 17L, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 15L, 15L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
16L, NA, NA, NA, NA, 20L, 34L, 31L, 33L, 34L, 34L, 34L, 34L,
34L, 34L, 34L, 34L, 34L, 34L, 34L, 34L, NA, NA, NA, NA, NA,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, NA, NA, NA, NA, NA, 22L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, NA, NA,
NA, NA, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, NA, NA, NA, NA, 6L, 8L, 8L,
8L, 8L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, NA, NA,
NA, NA, 11L, NA, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, NA, NA, NA, 12L, 5L, NA, 12L,
12L, 5L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
12L, NA, NA, NA, NA, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, 20L, 20L, 18L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, NA, NA, NA, NA, 27L, 24L,
21L, 14L, 27L, 14L, 21L, 27L, 27L, 14L, 27L, 27L, 27L, 27L,
27L, 27L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 68L, 73L,
78L, 54L, 79L, 76L, 87L, 72L, 62L, 63L, NA, NA, NA, NA, NA,
27L, 27L, 27L, 28L, 27L, 27L, 64L, 27L, 64L, 64L, 27L, 27L,
27L, 27L, 27L, NA, NA, NA, NA, NA, 18L, 20L, 18L, 20L, 20L,
18L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, NA, NA,
NA, NA, NA, 15L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, 9L, 7L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, NA, NA, NA, NA, NA, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, NA, NA, NA, NA, NA, 35L, 29L, 35L, 35L, 30L, 35L,
32L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 11L, 19L, 19L,
19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 19L, 19L, 20L, 11L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L,
20L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 16L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 33L, 33L, 32L, 33L, 33L, 33L, 33L, 33L, 33L, 33L,
33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, 33L, NA, 21L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L, 22L, 22L, 19L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 19L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 8L, 8L,
7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 11L, NA, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, 7L, 15L, 15L, 13L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, 27L, 19L, 27L, 27L, 27L,
27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L,
27L, 27L, NA, 76L, 23L, 23L, 23L, 32L, 65L, 32L, 28L, 32L,
28L, 32L, 32L, 23L, 28L, 32L, 28L, 28L, 32L, 84L, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, 14L, 18L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 15L,
NA, NA, 15L, NA, 15L, NA, NA, 15L, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, 9L, NA, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, NA, 28L, 36L, 36L, NA, 36L, 36L, 36L,
36L, NA, 36L, NA, 36L, 36L, 36L, 36L, 36L, NA, 36L, 36L,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
1L, 8L, 18L, 16L, 15L, 14L, 15L, 16L, 15L, 16L, 14L, 15L,
14L, 14L, 14L, 14L, 16L, 16L, 16L, 16L, 31L, 28L, 31L, 31L,
32L, 32L, 32L, 33L, 31L, 33L, 32L, 31L, 32L, 32L, 32L, 32L,
32L, 32L, 32L, 32L, 7L, 18L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
19L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 5L, 6L, 6L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 12L, 11L, 12L,
12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,
12L, 12L, 12L, 12L, 12L, 5L, 7L, 7L, 7L, 7L, 11L, 11L, 7L,
11L, 15L, 15L, 11L, 7L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
1L, 2L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 4L, 20L, 17L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 1L, 2L, 1L, 1L,
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 1L, 15L, 6L, 22L, 13L, 14L, 13L, 14L, 13L, 14L, 14L,
27L, 27L, 14L, 14L, 27L, 14L, 27L, 14L, 27L, NA, 15L, 20L,
20L, 20L, 20L, 40L, 20L, 40L, 20L, 40L, 40L, 40L, 40L, 20L,
40L, 40L, 40L, 40L, 32L, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 15L, 14L,
17L, 17L, 17L, 19L, 17L, 13L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 17L, 17L, 5L, 3L, 1L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 5L, 3L,
1L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L,
8L, 8L, 8L, 12L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, NA,
2L, 3L, 2L, 29L, 33L, 33L, 35L, 33L, 35L, 35L, 33L, 35L,
35L, 33L, 35L, 35L, 35L, 35L, 35L)), class = "data.frame", row.names = c(NA,
-1320L))
I believe the loess should be done on a split on the "software".
software <- unique(data2$software)
data_loess <- do.call(rbind, lapply(software, \(x) {
X <- subset(data2, software == x)
lo <- loess(count ~ samplexxx, X)
count_pred <- predict(lo, newdata=X)
return(cbind(X, count_pred))
}))
Note: R version 4.1.2 (2021-11-01)
Gives:
head(data_loess[data_loess$samplexxx > 80, ], 10)
# samplexxx software gene count count_pred
# 17 85 EH AFF2 24 22.69004
# 18 90 EH AFF2 24 22.31879
# 19 95 EH AFF2 24 21.83428
# 20 100 EH AFF2 24 21.25618
# 37 85 EH AR 21 22.69004
# 38 90 EH AR 21 22.31879
# 39 95 EH AR 21 21.83428
# 40 100 EH AR 21 21.25618
# 57 85 EH ATN1 NA 22.69004
# 58 90 EH ATN1 NA 22.31879
And here a plot of "count" predictions on "samplexxx".
plot(count_pred ~ samplexxx, data_loess, col=as.numeric(software) + 1,
pch=20, xlab='Downsampling', ylab='Count (LOESS)')
legend('topleft', legend=software, pch=19, col=as.numeric(software) + 1,
horiz=TRUE, cex=.7, title='Software')
Looks interesting, but I'm not sure if it's absolutely right.
In my answer you see something different from for loops, which is probably new to you, however it's the r-ish way and its much shorter to code. The looping job here does lapply().
Anyway, hope this helps.

Creating a custom legend with a subset of data ggplot [duplicate]

This question already has an answer here:
Remove legend entries for some factors levels
(1 answer)
Closed 3 years ago.
I am creating some stacked barplots in which there are about 50 different factors. I would like a legend that just maps the colors for the 8 most abundant factors.
I first calculated the mean abundance. Then I have ordered the factor by this. And can also get the corresponding colors, but I don't know if I should 'independently' create a legend, or if I am missing another 'easy' way with ggplot.
Any help appreciated.
thanks
## calculating the OTUs mean abundance
## instead of labelling all 50 in the legend just label top 5 or 10 for label
meanAbund<-as.data.frame(colSums(dat.grouped[,grep("Otu",colnames(dat.grouped))]))
meanAbund$Name<-as.character(tax_tab1[match(rownames(meanAbund),rownames(tax_tab1)),ncol(tax_tab1)])
colnames(meanAbund)<-c("mean_abund","Name")
top8_meanAbund<-meanAbund[rev(order(meanAbund$mean_abund)),][1:8]
# use melted dataframe for plotting
## now ordered by mean abundance
dat.groupedM$Level<-factor(dat.groupedM$Level,meanAbund[rev(order(meanAbund$mean_abund)),"Name"])
#top8 (mean is greater than 0.1 %)
# top 8 colors
library(RColorBrewer)
n <- length(unique(dat.groupedM$Level))
# generate divergent color palete, cause so many colors
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
set.seed(200)
mycols<-sample(col_vector, n)
top8cols<-mycols[1:8]
#pie(rep(1,n), mycols)
ggplot(dat.groupedM, aes(x = Time, y = value, fill = Level))+
geom_bar(stat = "identity") +
facet_wrap(~Diet)+
scale_fill_manual(values = mycols) +
theme_bw()+
theme(legend.position = "none")+
ggtitle(paste(level,"composition - Cohort 1"))
thanks getting closer now I have this, see below. But it isn't using my divergent palette "mycols" which I had specified with scale_fill_manual before now I changed to this as per suggestion. Okay now this is correct !!
scale_fill_manual(values = mycols,breaks = top10_meanAbund$Name)+
> dput(dat.groupedM)
structure(list(Diet = structure(c(2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 2L, 2L, 3L,
3L), .Label = c("Control", "RC", "WD"), class = "factor"), Time = structure(c(2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L), .Label = c("Control", "ZT2", "ZT14"
), class = "factor"), variable = structure(c(1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L,
6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L,
10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L,
13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L,
16L, 16L, 17L, 17L, 17L, 17L, 18L, 18L, 18L, 18L, 19L, 19L, 19L,
19L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L,
23L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 26L,
26L, 26L, 26L, 27L, 27L, 27L, 27L, 28L, 28L, 28L, 28L, 29L, 29L,
29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 31L, 31L, 32L, 32L, 32L,
32L, 33L, 33L, 33L, 33L, 34L, 34L, 34L, 34L, 35L, 35L, 35L, 35L,
36L, 36L, 36L, 36L, 37L, 37L, 37L, 37L, 38L, 38L, 38L, 38L, 39L,
39L, 39L, 39L, 40L, 40L, 40L, 40L, 41L, 41L, 41L, 41L, 42L, 42L,
42L, 42L, 43L, 43L, 43L, 43L, 44L, 44L, 44L, 44L, 45L, 45L, 45L,
45L, 46L, 46L, 46L, 46L, 47L, 47L, 47L, 47L, 48L, 48L, 48L, 48L,
49L, 49L, 49L, 49L, 50L, 50L, 50L, 50L), .Label = c("Otu1", "Otu108",
"Otu11", "Otu112", "Otu136", "Otu14", "Otu155", "Otu157", "Otu158",
"Otu161", "Otu182", "Otu186", "Otu197", "Otu21", "Otu23", "Otu242",
"Otu244", "Otu247", "Otu27", "Otu29", "Otu30", "Otu314", "Otu35",
"Otu36", "Otu378", "Otu4", "Otu40", "Otu42", "Otu427", "Otu44",
"Otu464", "Otu49", "Otu53", "Otu535", "Otu56", "Otu585", "Otu607",
"Otu623", "Otu629", "Otu645", "Otu648", "Otu664", "Otu69", "Otu715",
"Otu730", "Otu741", "Otu76", "Otu77", "Otu86", "Otu90"), class = "factor"),
value = c(0.125797907894198, 0.236708006778536, 0.577822547980787,
0.590703405992419, 0.010616635104027, 0.0101758392492056,
0.000833768625886666, 0.00075132991625995, 3.6675879491077e-05,
4.75000300636826e-05, 1.80354502712558e-05, 7.12272349413578e-06,
0.0923297961192989, 0.0516121598003722, 0.00943059557285678,
0.0071906839719107, 0.00539229454875785, 0.00506484304043506,
0.00338347504700533, 0.0025680210124108, 0.00175591025013762,
0.00395104856215105, 0.0561412864297836, 0.0389581641347799,
0.000170273382201598, 0.00010844375756416, 2.43702775724318e-05,
2.69013349522259e-05, 0.00832912099453767, 0.010385453199374,
0.000178806881780292, 0.000192961017676232, 0.000133411286157921,
0.000160277350764036, 3.61247330219488e-05, 2.18172717187001e-05,
0.0052992653709469, 0.0157284378186556, 1.02095850472487e-05,
6.26578426928999e-06, 1.60700750910741e-05, 1.5642472562587e-05,
6.62816031320301e-06, 0.00184183762620945, 0.000976314979621793,
0.000837378482800852, 0.00119405390180218, 0.000749043101546972,
2.53563183604468e-05, 6.40671433657518e-05, 2.15845735655314e-05,
2.23193546150843e-05, 0.021152108912735, 0.0154293683430873,
0.0179088127298003, 0.0243504748685249, 0.112274814726721,
0.117619628857172, 3.02064928526444e-05, 4.05741755377207e-05,
0.00181223384695308, 0.00207625195815772, 0.000943789542460111,
0.000206467245724716, 0.00154532777776536, 0.00226885210972427,
0.000119002475328241, 0.00022113732768583, 0.000235485770787934,
0.000458323057092208, 0.000652960109256795, 0.000724862646259261,
0.0727879614169974, 0.0343552622468531, 0.00966883214135748,
0.0121723948692721, 0.0502079899784375, 0.0642059286182179,
0.0744606748095006, 0.0279356500162451, 0.0165712179668264,
0.0155282557608783, 0.0161360297824822, 0.0176198016904319,
0.0025636247608102, 0.0011990003339988, 8.03074966867612e-05,
2.33672477744522e-05, 0.082133947866647, 0.000268818474649765,
9.9394282675768e-05, 5.50800067064597e-05, 0.0740561864383357,
0.0623723308152442, 0.0122016944534841, 0.00661733731518039,
0.000206774473028281, 0.000181997559545235, 0.000504582984323445,
0.0003864059666649, 0.260050134018791, 0.262172946886686,
0.18452199172589, 0.173786000484964, 0.0269969369566207,
0.0314904830827211, 0.00193643447967831, 0.00224489247051206,
3.93537896032742e-05, 1.28428312370815e-05, 0.0088546261393493,
0.0167354308377304, 1.21169704358824e-05, 2.12185497965253e-05,
6.62816031320301e-06, 1.43770979648094e-05, 1.55017664132774e-05,
4.91659313365037e-05, 0.000125001966670021, 6.22422609777641e-05,
2.67226640566305e-05, 3.7715397236691e-05, 0.000156595002030591,
0.000177342276671081, 9.9289511018095e-05, 3.26074531511788e-05,
0.0133283089983016, 0.016339336685079, 0.000374046362264717,
0.000314832095026693, 0.000101840989635774, 0.0499536313744285,
3.07770376000906e-05, 2.61927046816827e-05, 6.62816031320301e-06,
6.26578426928999e-06, 0.0190857963424119, 0.033561743200736,
0.00670074972877479, 0.00537788085712994, 1.18971385403729e-05,
1.11445994651961e-05, 6.62816031320301e-06, 6.26578426928999e-06,
1.14712208113288e-05, 2.05354865936513e-05, 7.60426873897666e-06,
6.26578426928999e-06, 1.20062319150955e-05, 1.36539983715138e-05,
6.62816031320301e-06, 7.2222843532018e-06, 9.9140609239925e-06,
9.94926827158573e-06, 7.53483093323745e-06, 8.69321376638133e-06,
1.21169704358824e-05, 1.19091870744721e-05, 6.62816031320301e-06,
7.23507396088365e-06, 2.46118496456816e-05, 2.17587837491135e-05,
6.62816031320301e-06, 6.26578426928999e-06, 1.82559375344064e-05,
1.89730194735652e-05, 6.62816031320301e-06, 6.26578426928999e-06,
0.00660850850197291, 0.0212222385456563, 0.00211118341459913,
0.00141420689575609, 9.26797200368037e-06, 8.90032999685065e-06,
7.54855398500617e-06, 6.26578426928999e-06, 2.23089983289096e-05,
2.17587837491135e-05, 6.62816031320301e-06, 6.26578426928999e-06,
5.45457596965578e-06, 5.45457596965578e-06, 6.62816031320301e-06,
5.98284905868666e-06, 3.2907497931271e-05, 2.32160410324433e-05,
6.62816031320301e-06, 1.51092819784857e-05, 1.21169704358824e-05,
1.19091870744721e-05, 7.91517227728171e-06, 7.23507396088365e-06,
4.18664545392701e-05, 4.14341191547126e-05, 0.000151073775168509,
0.000399628089283355, 9.9140609239925e-06, 1.4300121286468e-05,
7.53483093323745e-06, 6.26578426928999e-06), Level = structure(c(1L,
1L, 1L, 1L, 25L, 25L, 25L, 25L, 3L, 3L, 3L, 3L, 7L, 7L, 7L,
7L, 28L, 28L, 28L, 28L, 9L, 9L, 9L, 9L, 31L, 31L, 31L, 31L,
27L, 27L, 27L, 27L, 30L, 30L, 30L, 30L, 26L, 26L, 26L, 26L,
42L, 42L, 42L, 42L, 39L, 39L, 39L, 39L, 11L, 11L, 11L, 11L,
13L, 13L, 13L, 13L, 4L, 4L, 4L, 4L, 33L, 33L, 33L, 33L, 36L,
36L, 36L, 36L, 43L, 43L, 43L, 43L, 6L, 6L, 6L, 6L, 5L, 5L,
5L, 5L, 15L, 15L, 15L, 15L, 38L, 38L, 38L, 38L, 10L, 10L,
10L, 10L, 8L, 8L, 8L, 8L, 45L, 45L, 45L, 45L, 2L, 2L, 2L,
2L, 16L, 16L, 16L, 16L, 24L, 24L, 24L, 24L, 44L, 44L, 44L,
44L, 18L, 18L, 18L, 18L, 46L, 46L, 46L, 46L, 20L, 20L, 20L,
20L, 12L, 12L, 12L, 12L, 47L, 47L, 47L, 47L, 17L, 17L, 17L,
17L, 32L, 32L, 32L, 32L, 48L, 48L, 48L, 48L, 49L, 49L, 49L,
49L, 50L, 50L, 50L, 50L, 34L, 34L, 34L, 34L, 29L, 29L, 29L,
29L, 40L, 40L, 40L, 40L, 19L, 19L, 19L, 19L, 35L, 35L, 35L,
35L, 37L, 37L, 37L, 37L, 41L, 41L, 41L, 41L, 14L, 14L, 14L,
14L, 21L, 21L, 21L, 21L, 23L, 23L, 23L, 23L, 22L, 22L, 22L,
22L), .Label = c("Akkermansia", "Bacteroides", "Pseudomonas",
"Anaeroplasma", "Acetatifactor", "Lactobacillus", "Clostridium_XlVa",
"Oscillibacter", "Eubacterium", "Alistipes", "Acinetobacter",
"Parabacteroides", "Parasutterella", "Bacillus", "Clostridium_sensu_stricto",
"Turicibacter", "Clostridium_IV", "Staphylococcus", "Bifidobacterium",
"Romboutsia", "Escherichia/Shigella", "Listeria", "Enterococcus",
"Lactococcus", "Flavonifractor", "Ruminococcus", "Lachnospiracea_incertae_sedis",
"Clostridium_XlVb", "Stenotrophomonas", "Eisenbergiella",
"Hungatella", "Adhaeribacter", "Butyricicoccus", "Rhizobium",
"Prevotella", "Intestinimonas", "Sphingobium", "Dorea", "Enterorhabdus",
"Shewanella", "Bradyrhizobium", "Desulfovibrio", "Clostridium_XVIII",
"Anaerostipes", "Asaccharobacter", "Anaerotruncus", "Eggerthella",
"Butyricimonas", "Bilophila", "Anaerococcus"), class = "factor")), row.names = c(2L,
3L, 4L, 5L, 7L, 8L, 9L, 10L, 12L, 13L, 14L, 15L, 17L, 18L, 19L,
20L, 22L, 23L, 24L, 25L, 27L, 28L, 29L, 30L, 32L, 33L, 34L, 35L,
37L, 38L, 39L, 40L, 42L, 43L, 44L, 45L, 47L, 48L, 49L, 50L, 52L,
53L, 54L, 55L, 57L, 58L, 59L, 60L, 62L, 63L, 64L, 65L, 67L, 68L,
69L, 70L, 72L, 73L, 74L, 75L, 77L, 78L, 79L, 80L, 82L, 83L, 84L,
85L, 87L, 88L, 89L, 90L, 92L, 93L, 94L, 95L, 97L, 98L, 99L, 100L,
102L, 103L, 104L, 105L, 107L, 108L, 109L, 110L, 112L, 113L, 114L,
115L, 117L, 118L, 119L, 120L, 122L, 123L, 124L, 125L, 127L, 128L,
129L, 130L, 132L, 133L, 134L, 135L, 137L, 138L, 139L, 140L, 142L,
143L, 144L, 145L, 147L, 148L, 149L, 150L, 152L, 153L, 154L, 155L,
157L, 158L, 159L, 160L, 162L, 163L, 164L, 165L, 167L, 168L, 169L,
170L, 172L, 173L, 174L, 175L, 177L, 178L, 179L, 180L, 182L, 183L,
184L, 185L, 187L, 188L, 189L, 190L, 192L, 193L, 194L, 195L, 197L,
198L, 199L, 200L, 202L, 203L, 204L, 205L, 207L, 208L, 209L, 210L,
212L, 213L, 214L, 215L, 217L, 218L, 219L, 220L, 222L, 223L, 224L,
225L, 227L, 228L, 229L, 230L, 232L, 233L, 234L, 235L, 237L, 238L,
239L, 240L, 242L, 243L, 244L, 245L, 247L, 248L, 249L, 250L), class = "data.frame")
I couldn't get your code to run, so I'll answer your question with dummy data instead.
Let's generate some unequally distributed data, letters in this case.
set.seed(0)
df <- data.frame(x = LETTERS[c(rpois(100, 1) + 1, rpois(100, 8) + 1)])
We can determine the 8 most frequently occuring letters:
most_freq <- names(tail(sort(table(df$x)), 8))
Which we can then put into any of the discrete scales functions (including the manual one) as the breaks argument:
ggplot(df, aes(x, fill = x)) +
geom_bar() +
scale_fill_discrete(breaks = most_freq)
And as you can see, the categories not in the breaks still get a colour but don't get mentioned in the legend.

Use rbind() in nested for loop with apply() in r

How can you use rbind in a for loop that runs through a list of dataframes? I tried to follow Looping through list of data frames in R but receive the following:
Error in apply(dataFramesList, 2, function(x) { :
dim(X) must have a positive length
I have two dataframes, dfTraining and dfAccuracy (code to reproduce dataframes is below), and need to add a row for any of the crop types missing from either of two columns, CROP or CROP_LABEL. I believe my problem is in my last line of code.
My code block is:
dataFramesList <- list(dfTraining, dfAccuracy)
apply(dataFramesList, 2, function(x){
cropNumbers <- seq(1,23, by = 1)
cropNumbers <- cropNumbers[-c(3)]
cropNumbers <- append(cropNumbers, 34)
listofCROPandCROP_LABELColumns <- list(dataFrameList$CROP, dataFrameList$CROP_LABEL)
missingCROP <- NULL
for (i in listofCROPandCROP_LABELColumns){
for (j in cropNumbers){
if (!j %in% i){
# If crop number is missing from CROP_LABEL, add missingCROP observation (row)
# Make row for missing crop type
missingCrop <- list(FREQUENCY = 0, AA = 1, CROP = j, CROP_LABEL = j, ACRES = 0)
dataFrameList <- rbind(dataFrameList, missingCrop)
}
}
}
})
My dfAccuracy dataframe:
structure(list(FREQUENCY = c(4L, 2L, 1L, 1L, 1L, 1L, 65L, 1L,
1L, 4L, 1L, 5L, 5L, 2L, 4L, 1L, 1L, 1L, 1L, 4L, 9L, 2L, 1L, 1L,
1L, 2L, 4L, 1L, 2L, 18L, 1L, 10L, 3L, 1L, 7L, 1L, 1L, 1L, 3L,
1L, 7L, 1L), AA = c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L),
CROP = c(1L, 4L, 12L, 13L, 14L, 18L, 1L, 1L, 1L, 1L, 1L,
4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 13L,
13L, 13L, 13L, 14L, 14L, 14L, 18L, 18L, 18L, 18L, 18L, 19L,
19L, 21L, 21L, 21L, 21L), CROP_LABEL = c(1L, 4L, 14L, 13L,
12L, 18L, 1L, 4L, 5L, 6L, 18L, 1L, 4L, 6L, 14L, 18L, 12L,
14L, 18L, 1L, 6L, 14L, 18L, 18L, 4L, 6L, 13L, 21L, 12L, 14L,
18L, 1L, 6L, 14L, 18L, 21L, 1L, 19L, 6L, 13L, 21L, 34L),
ACRES = c(331.737184484, 193.772138572, 26.48543619, 73.2696289437,
112.470306056, 66.6556450342, 3905.71121736, 24.9581079934,
39.9287379709, 259.662359273, 85.2786247851, 306.051491303,
368.342995232, 154.82030835, 265.754349805, 70.3722566979,
35.4066607701, 139.336463432, 58.4307705147, 251.070357093,
471.031628349, 150.965736858, 28.2780117926, 35.3426930108,
34.5730542194, 67.7383953308, 144.442123948, 33.2746560126,
69.4072817311, 1219.65459596, 92.4840910734, 582.983473317,
191.957841327, 35.708775262, 319.638682538, 60.6889287642,
82.6244195055, 36.2898952104, 267.422844756, 72.8352758659,
489.746546145, 65.5392893502)), row.names = c(25L, 26L, 27L,
29L, 30L, 31L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L,
70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L,
83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L
), class = "data.frame")
and my dfTraining dataframe is:
structure(list(FREQUENCY = c(7L, 1L, 1L, 4L, 2L, 6L, 1L, 107L,
1L, 21L, 1L, 1L, 1L, 2L, 1L, 19L, 3L, 1L, 1L, 12L, 1L, 2L, 32L,
2L, 2L, 29L, 2L, 18L, 1L), AA = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L), CROP = c(1L, 1L, 4L, 4L, 12L, 13L, 21L,
1L, 1L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 7L, 12L, 13L, 14L, 14L,
14L, 18L, 18L, 18L, 19L, 21L, 34L), CROP_LABEL = c(1L, 4L, 1L,
4L, 12L, 13L, 21L, 1L, 6L, 4L, 6L, 1L, 5L, 14L, 18L, 6L, 14L,
1L, 12L, 13L, 1L, 6L, 14L, 6L, 14L, 18L, 19L, 21L, 34L), ACRES = c(624.940370218,
26.9188766351, 37.8773839813, 291.79294767, 140.949264214, 391.571023675,
44.5217011939, 6806.02216989, 72.7500299887, 1676.12121152, 14.8739557721,
67.0700291739, 59.7438207953, 82.6713019474, 75.62666152, 1370.78710769,
145.215281276, 41.7380537313, 66.5236760194, 679.91208779, 70.9661875374,
38.8514254734, 1749.63365551, 109.917242057, 79.7758083723, 1660.85759895,
96.8771921798, 1428.71888481, 69.473161379)), row.names = c(18L,
19L, 20L, 21L, 22L, 23L, 24L, 38L, 39L, 40L, 41L, 42L, 43L, 44L,
45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L,
58L, 59L), class = "data.frame")

R and NLS: singular gradient matrix at initial parameter

I'm trying to use nls to estimate the parameters of a non linear model.
I first use nls2 to find good initial parameters with Random Search and I then use nls to improve the estimation with a Gauss-Newton approach.
The problem is I always get an "singular gradient matrix at initial parameter estimates" error.
I'm not sure I understand, because the input matrix doesn't seem to be a singular gradient matrix.
Moreover even if the fits I'm looking for is not perfect for this data, nls should find a way to improve the
parameters estimations. Isn't it ?
Question: Is there a way to improve the parameters estimation?
I've tried NLS.lm but I had the same problem.
Here is a reproductible example:
Data:
structure(list(x1 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L), x2 = c(1L, 2L, 3L, 4L,
5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L,
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L,
32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L,
45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L,
58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 0L, 1L, 2L,
3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L,
17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L,
30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L,
43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L,
56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 0L, 1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L,
29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L,
42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L,
55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 0L, 1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L,
29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L,
42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L,
55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 0L, 1L, 2L,
3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L,
17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L,
30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L,
43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L,
56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 0L, 1L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L,
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L,
32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L,
45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L,
58L, 59L, 60L, 61L, 62L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L,
22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L,
35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L,
48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L,
61L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L,
14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L,
27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L,
40L, 41L, 42L, 43L, 44L, 45L), y = c(0.0689464583349188, 0.0358227182166929,
0.0187034836294036, 0.0227081421239796, 0.0146603483536504, 0.00562771204350896,
0.00411351161052011, 0.00356917888321555, 0.0028017552960605,
0.0024750328652541, 0.00243175013170564, 0.00242654283706898,
0.00235224917236107, 0.00176144220485858, 0.00138071934398105,
0.000696375069179013, 0.00106282865382483, 0.00114735219137874,
0.00277256441625284, 0.00214359572321392, 0.00144935953386591,
0.00249732559162499, 0.00225859018399108, 0.00201642941663214,
0.00232438586834105, 0.0016083751355862, 0.00143118376291818,
0.00158323933266031, 0.00157585431454131, 0.00169206800399143,
0.00158514119474578, 0.00134506293557103, 0.00119442163345335,
0.00101284069499962, 0.0012621113004254, 0.00128964367655383,
0.00102819258807122, 0.00125345601171754, 0.00116155619985178,
0.00142466624262548, 0.00141075318725309, 0.00106556656123991,
0.0010976347045814, 0.0012442089226047, 0.0010627617251863, 0.00125322168410487,
0.00112108560656369, 0.0012459199320756, 0.00135773322693401,
0.0013997982284804, 0.00155012485145915, 0.00151108062240688,
0.00149570655260348, 0.00152598641103596, 0.00108261570337346,
0.000992225418429453, 0.000769588971038765, 0.000700496873143604,
0.000688378351958078, 0.000595007407260441, 0.000557615594951187,
0.00040476923690092, 0.000492276455560289, 0.000447248723966691,
0.000388694992851599, 0.000346087542525691, 0.000189803623801549,
0.0709302325562937, 0.0424623423412875, 0.019085896698975, 0.0190650552541205,
0.014276898897581, 0.00593407290200902, 0.00445528598343583,
0.00371231334350143, 0.00253909496678967, 0.00263487912423124,
0.00248012072619926, 0.00263786771266913, 0.00219351150766708,
0.00179271674850348, 0.00139646119589996, 0.000911560061336614,
0.000989537441246412, 0.001046390000492, 0.00223993432619926,
0.00164189356162362, 0.00106041866437064, 0.00194151698794588,
0.0014213192200082, 0.00165239495268553, 0.00196583929282493,
0.00120501090643706, 0.001141403899631, 0.00122398595424354,
0.00124538223829438, 0.00123370121853218, 0.00136883147552275,
0.00110907318146781, 0.000965843164247642, 0.000859986264862649,
0.00104695561918819, 0.00103985460139401, 0.000455832014104141,
0.000704296760639607, 0.000870145383845838, 0.000919870911357114,
0.00101396309667897, 0.000781894087412874, 0.000909712365723658,
0.000889897365477655, 0.000933063039278393, 0.000779395399425994,
0.000789546295038951, 0.000773432990897909, 0.00125614787798278,
0.00123172652693727, 0.00078936677195572, 0.000952107503075031,
0.00105449131480115, 0.00123128091742517, 0.000889501370397704,
0.00085648642099221, 0.000830097733497335, 0.000653482256334563,
0.000521696831160312, 0.000612702433456335, 0.000513576588109881,
0.000475289330709307, 0.00041141913800738, 0.000328157997211972,
0.00031336264403444, 0.000328784093808938, 0.000237448446412464,
0.0520691145678866, 0.0281929482152033, 0.0219024230330532, 0.0141074098760277,
0.00691341703402584, 0.00445785262213699, 0.0034569415664917,
0.00234406584844369, 0.00257369504707459, 0.00234047371531346,
0.00227286083862502, 0.00248544382019894, 0.00180810413760828,
0.00138986347039715, 0.000911936124008956, 0.000932783218782117,
0.00108887529088974, 0.0017855660833578, 0.00159768589505946,
0.00124091041330201, 0.00203036436876009, 0.00154489107876964,
0.00111687975012847, 0.00163256939968433, 0.00143626193198502,
0.000996683818914256, 0.0010781399542101, 0.00122575793431581,
0.00115671467616723, 0.001069532453476, 0.0010106869893371, 0.000978618104445015,
0.000894478048836441, 0.000842874700392747, 0.000819009288742475,
0.000843003919670386, 0.000964158733115548, 0.000877802228013507,
0.00087592051873807, 0.000935810596369843, 0.000879047729316546,
0.000829181439950081, 0.0010295792954412, 0.000765620227389517,
0.00102511256239906, 0.000823109180461753, 0.00111669534392894,
0.000802757620485245, 0.00103231207284173, 0.000884354083467919,
0.00109278942886507, 0.000969283099489796, 0.000827480664091176,
0.000798564447676552, 0.000909248326695786, 0.000682209033640434,
0.000780593294853913, 0.000485172195712818, 0.000467514093470122,
0.000295219649739392, 0.000460636351123183, 0.00045060371687344,
0.000492590160218764, 0.000402536549331963, 0.000271941766535751,
0.000171012123770371, 0.0267385565244063, 0.0275426278720772,
0.0154589149018475, 0.00729065000152096, 0.00513675524527996,
0.00378848397112206, 0.00305965140790087, 0.00240428827949139,
0.00233604733730811, 0.00199601458903693, 0.00198302547453915,
0.00137121122011316, 0.00126241982975401, 0.0012413298189045,
0.00103044327584109, 0.00106759120581615, 0.00190957422380402,
0.00124400301656831, 0.000989035353673623, 0.00160702520431547,
0.0011515826661394, 0.00153203681379408, 0.00134897491229138,
0.000916492937174261, 0.00072393419977287, 0.00115124473393361,
0.00104241370079698, 0.000953324905193568, 0.00121656899373365,
0.000891420608484922, 0.000671666092758208, 0.000659860761797571,
0.000586145968952161, 0.00072735268499929, 0.000658407622538582,
0.000498831767252743, 0.000658345030520574, 0.000542106922897528,
0.000874560054044737, 0.000543320226217274, 0.000751139509440084,
0.000668632963233356, 0.000656903021131188, 0.000574965903652329,
0.0006661524076778, 0.000605171890653201, 0.000527045917239561,
0.000985791370586684, 0.000899420142057553, 0.000933015548254953,
0.00082137283567561, 0.000870124781995904, 0.000498046123582973,
0.000540181050881142, 0.000596948101336416, 0.000405622486362069,
0.000631594016548032, 0.000468749313033603, 0.000389576698910993,
0.000335624642574679, 0.000286763668856847, 0.000439039581432135,
0.000244767908276044, 0.000303911794528604, 0.000160988671898765,
0.0365772382134747, 0.0255898183301035, 0.010327803963121, 0.00714710822108354,
0.00506253612461807, 0.00447056668291465, 0.00322822676102386,
0.00328154620569948, 0.0028470908747756, 0.00253477302081723,
0.00187837758253778, 0.00116416512964702, 0.00119557763663167,
0.000993575112051645, 0.00136274483135782, 0.00204131052512691,
0.00157953945941769, 0.00116523253183218, 0.00190793844827791,
0.00144595416523011, 0.00157423646879793, 0.00126996001866537,
0.00115283860342634, 0.00116894693507543, 0.000930041619012519,
0.00106545753272384, 0.00123507493015348, 0.00130865599847824,
0.000940647984853709, 0.000836521897923032, 0.000778436697656724,
0.00100773629284415, 0.000956581999215341, 0.000808036977042788,
0.000597930101173421, 0.000776453419209873, 0.000630241947142534,
0.000649832426616575, 0.000782188275296327, 0.00102823806308181,
0.000830656989407107, 0.00051915559901561, 0.000537114715917872,
0.000872430107712244, 0.000549284113632851, 0.000738257038745497,
0.00097442578198376, 0.000879724260815807, 0.000884543540237537,
0.00100038027474944, 0.00103543285342337, 0.000875585441608313,
0.000829083410412184, 0.000760316116414823, 0.000712211369823927,
0.000386744815307978, 0.000428331410721292, 0.000397681982571065,
0.000213938551710199, 0.000370800615243779, 0.000281234314553042,
0.000267359921177464, 0.000358376119030352, 0.000337361541022196,
0.0310029062887812, 0.0154963087949333, 0.00959302943445506,
0.00645674376405936, 0.00525321947702945, 0.00386084394749159,
0.00374364242039947, 0.00351047952579374, 0.00298556939927835,
0.00199158625919048, 0.00206559575086432, 0.00169077836254661,
0.00139156751815451, 0.00170363478493893, 0.00250481301085496,
0.00182474837251083, 0.00116804333227652, 0.00155778636185214,
0.00183778204100427, 0.00135012918459471, 0.00166904872503284,
0.00120137403943415, 0.00108307957787943, 0.00146041465872549,
0.0014437889563235, 0.000975926161359965, 0.00102580511345623,
0.00112145083941, 0.000921884915530595, 0.00082253191796126,
0.000634876416504371, 0.00108601324863747, 0.000830573067167897,
0.000965052460105379, 0.000922667052402736, 0.000863193817654785,
0.000982111173513293, 0.000763009170856168, 0.000921755812461313,
0.000771609983091022, 0.000669047474976222, 0.000773869648383834,
0.00072022523061129, 0.000742426347056781, 0.000718728249316847,
0.000761437280522971, 0.000833112611531319, 0.000794451658438637,
0.000907360341651947, 0.00112083735676435, 0.00102996529205731,
0.000651843453054939, 0.000640968179416338, 0.000549646466476441,
0.000778958256714525, 0.000627413038784969, 0.000523658918731223,
0.000418571973368359, 0.000643352520494588, 0.000351378727146459,
0.000504093577607682, 0.000333827596358531, 0.000339505558071773,
0.0181836504450303, 0.0135527124187004, 0.00780738765319868,
0.00643260738080874, 0.00476881905655232, 0.00406986745617877,
0.00400325917456592, 0.00277499160186111, 0.00198311377238581,
0.00241837807740304, 0.00141018451525995, 0.00166798657140732,
0.0013970042073337, 0.00237332662413329, 0.00146721126831566,
0.000990562316636778, 0.00186106889002752, 0.00186322276224556,
0.00140391140302307, 0.00139027556176293, 0.00125730361478641,
0.00127044200804939, 0.00126655503830484, 0.00133956330669488,
0.00128219844136096, 0.00109531452608613, 0.00112195611926977,
0.00101411381866565, 0.00104786051750783, 0.000798711632769435,
0.000852432172756047, 0.000852720107765923, 0.00110385307389073,
0.00081385514739304, 0.00102898862672826, 0.000710330768658628,
0.000803425598538879, 0.000723455383750816, 0.00075034248654992,
0.000864917906994041, 0.000799733114881449, 0.000608518601191706,
0.000855476747683942, 0.000988548021123443, 0.00104800683206201,
0.000997051779707941, 0.000796235203259423, 0.000910577791459715,
0.000869997383535945, 0.000557402535474327, 0.000757813148434336,
0.000480807445269952, 0.000553425518375578, 0.000633029237291637,
0.00050222863978579, 0.000390945889771328, 0.000430333228928208,
0.000425167676834459, 0.000239604519722651, 0.000357021364759551,
0.000292330910803864, 0.000288851701197491, 0.0198837196044917,
0.0142208140311702, 0.00733039271103269, 0.00609158853724431,
0.00487605866828399, 0.00382636157210858, 0.00411545257392807,
0.00235906433257981, 0.00228491326937568, 0.00109255715480326,
0.00158036861847788, 0.00122011020381908, 0.00223761733564904,
0.00173284341769128, 0.00117538923471357, 0.00219622963095698,
0.00214263916211795, 0.0013198229549172, 0.00172951959530242,
0.00128074705482347, 0.00124062569884766, 0.00144218669111025,
0.00148407512819099, 0.00100716026446858, 0.0010842890711437,
0.000800686408079248, 0.000890454658065465, 0.000887152794471706,
0.00105780722647994, 0.000874948318354744, 0.000569126715186268,
0.000924642167943982, 0.000857013884141074, 0.000823122890591976,
0.00073038777177409, 0.000522615873628494, 0.00070936497950782,
0.000823074755104667, 0.000720588701733105, 0.000722724038337836,
0.00063458965098969, 0.000620049346639466, 0.000842327487089008,
0.000617708212493797, 0.000783953750160813, 0.00112567150392384
)), .Names = c("x1", "x2", "y"), class = c("tbl_df", "data.frame"
), row.names = c(NA, -500L))
Initial parameters: initial_par
structure(list(A1 = 0.0529486559121727, alpha1 = 0.00888818269595504,
B1 = 0.250994319084551, beta1 = 0.471984946168959, A2 = 0.281956987357551,
alpha2 = 0.325086771510541, B2 = 0.0562204262765557, beta2 = 0.725645614322275), class = "data.frame", row.names = c(NA,
-1L), .Names = c("A1", "alpha1", "B1", "beta1", "A2", "alpha2",
"B2", "beta2"))
Formula:
formula = y ~
(A1*exp(-alpha1*x1) + B1*exp(-beta1*x1)) *
(A2*exp(-alpha2*x2) + B2*exp(-beta2*x2))
Nls and the error message
final = nls(formula,
data=df,
start = as.list(as.vector(initial_par)))
Error in nlsModel(formula, mf, start, wts) :
singular gradient matrix at initial parameter estimates
The problem is that there is not a one to one relationship between your model and parameters. To see this write A1 = exp(a1+d), A2 = exp(a2-d), B1 = exp(b1+d), B2 = exp(b2-d) in which case we have:
y ~ exp(-alpha1 * x1 + a1 + d) * exp(-alpha2 * x2 + a2 - d) +
exp(-alpha1 * x1 + a1 + d) * exp(-beta2 * x2 + b2 - d) +
exp(-beta1 * x1 + b1 + d) * exp(-alpha2 * x2 + a2 - d) +
exp(-beta1 * x1 + b1 + d) * exp(-beta2 * x2 + b2 - d)
But d cancels in each of the 4 terms and so cancels entirely from the RHS. That is, the RHS is the same for any value of d thus the model is overparameterized and so will give a singular gradient.
Fix one of A1, A2, B1, B2 and then you should be able to get a solution:
A1 <- 1
nls(formula, df, start = initial_par[-1])
giving:
Nonlinear regression model
model: y ~ (A1 * exp(-alpha1 * x1) + B1 * exp(-beta1 * x1)) * (A2 * exp(-alpha2 * x2) + B2 * exp(-beta2 * x2))
data: df
alpha1 B1 beta1 A2 alpha2 B2 beta2
0.11902 1.21030 0.79076 0.04604 0.51697 0.00183 0.02317
residual sum-of-squares: 0.000685
Number of iterations to convergence: 11
Achieved convergence tolerance: 6.686e-06

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