Hey Carl,
I want to report an issue I found when running summarizeAlignments.
align.dir = "test_dir/"
align.summary <- summarizeAlignments(alignment.path = align.dir,
alignment.format = "phylip",
dataset.name = "Spheno_AHE",
file.export = "Sphenomorphini/Spheno_AHE.csv",
overwrite = TRUE)I keep getting a data.table error:
Error: Check that is.data.table(DT) == TRUE. Otherwise, :=, `:=`(...) and let(...) are defined for use in j, once only and in particular ways. See help(":=").
However, when I redefined the function with the exact code you've written (without any modifications), it works. Note that I just changed summarize to summarise to test it out.
summariseAlignments<-function (alignment.path = NULL, file.export = NULL, overwrite = FALSE,
dataset.name = NULL, alignment.format = c("phylip", "nexus"))
{
require(data.table)
if (is.null(alignment.path) == TRUE) {
stop("Error: no alignment path provided.")
}
if (is.null(dataset.name) == TRUE) {
stop("Error: a dataset name is needed.")
}
if (dir.exists(alignment.path) == F) {
return(paste0("Directory of alignments could not be found. Exiting."))
}
if (overwrite == TRUE) {
if (file.exists(paste0(file.export, ".csv")) == T) {
system(paste0("rm ", file.export, ".csv"))
}
}
else {
if (file.exists(paste0(file.export, ".csv")) == T) {
print(paste0("File exists for ", file.export, " and overwrite = FALSE. Exiting."))
save.data = read.csv(paste0(file.export, ".csv"))
return(save.data)
}
}
align.names = list.files(alignment.path)
header.data = c("dataset", "file", "number_samples", "proportion_samples",
"alignment_length", "count_pis", "proportion_pis", "count_missing_bp",
"proportion_missing_bp")
collect.data = data.table::data.table(matrix(as.numeric(0),
nrow = length(align.names), ncol = length(header.data)))
data.table::setnames(collect.data, header.data)
collect.data[, `:=`(file, as.character(file))]
collect.data[, `:=`(dataset, as.character(dataset))]
for (x in 1:length(align.names)) {
if (alignment.format == "phylip") {
align = ape::read.dna(paste0(alignment.path, "/",
align.names[x]), format = "sequential")
}
if (alignment.format == "nexus") {
align = ape::read.nexus.data(paste0(alignment.path,
"/", align.names[x]))
align = ape::as.DNAbin(matrix(unlist(align), ncol = length(align[[1]]),
byrow = TRUE))
}
data.table::set(collect.data, i = as.integer(x), j = match("dataset",
header.data), value = dataset.name)
data.table::set(collect.data, i = as.integer(x), j = match("file",
header.data), value = align.names[x])
data.table::set(collect.data, i = as.integer(x), j = match("number_samples",
header.data), value = nrow(align))
data.table::set(collect.data, i = as.integer(x), j = match("alignment_length",
header.data), value = ncol(align))
count.pis = PhyloConfigR::informativeSites(align, count = T,
ambiguities = T)
prop.pis = round(count.pis/ncol(align), 3)
data.table::set(collect.data, i = as.integer(x), j = match("count_pis",
header.data), value = count.pis)
data.table::set(collect.data, i = as.integer(x), j = match("proportion_pis",
header.data), value = prop.pis)
len.temp = as.character(as.list(align))
len.loci = lapply(len.temp, function(x) x[x != "-"])
len.loci = lapply(len.loci, function(x) x[x != "n"])
len.loci = lapply(len.loci, function(x) x[x != "?"])
spp.len = unlist(lapply(len.loci, function(x) length(x)))
miss.total = (max(spp.len) - spp.len)
miss.prop = round(sum(miss.total)/(max(spp.len) * nrow(align)),
3)
data.table::set(collect.data, i = as.integer(x), j = match("count_missing_bp",
header.data), value = sum(miss.total))
data.table::set(collect.data, i = as.integer(x), j = match("proportion_missing_bp",
header.data), value = miss.prop)
}
save.data = collect.data[collect.data$file != 0, ]
save.data[, `:=`(proportion_samples, round(number_samples/max(number_samples),
3))]
if (is.null(file.export) != TRUE) {
write.csv(save.data, file = paste0(file.export, ".csv"),
row.names = F)
}
return(save.data)
}align.summary <- summariseAlignments(alignment.path = align.dir,
alignment.format = "phylip",
dataset.name = "Spheno_AHE",
file.export = "Sphenomorphini/Spheno_AHE.csv",
overwrite = TRUE)The function works as expected. I'm not sure why, but thought I'd report it as an issue.
My session info:
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8 LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
time zone: Australia/Sydney
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.22 data.table_1.15.4 ape_5.7-1 PhyloConfigR_0.2.0
loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.4.0 crayon_1.5.2 promises_1.2.1 Rcpp_1.0.12 stringr_1.5.1 parallel_4.4.0 callr_3.7.3
[9] later_1.3.1 fastmap_1.2.0 lattice_0.22-6 mime_0.12 R6_2.5.1 curl_5.1.0 htmlwidgets_1.6.4 desc_1.4.2
[17] profvis_0.3.8 rprojroot_2.0.4 shiny_1.7.5.1 rlang_1.1.3 cachem_1.1.0 stringi_1.7.12 httpuv_1.6.12 fs_1.6.4
[25] pkgload_1.3.3 memoise_2.0.1 cli_3.6.2 magrittr_2.0.3 ps_1.7.5 grid_4.4.0 digest_0.6.33 processx_3.8.2
[33] rstudioapi_0.15.0 xtable_1.8-4 remotes_2.4.2.1 devtools_2.4.5 nlme_3.1-163 lifecycle_1.0.4 prettyunits_1.2.0 vctrs_0.6.4
[41] glue_1.7.0 urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.2 purrr_1.0.2 usethis_2.2.3 tools_4.4.0 ellipsis_0.3.2
[49] htmltools_0.5.8.1
Hey Carl,
I want to report an issue I found when running summarizeAlignments.
I keep getting a data.table error:
However, when I redefined the function with the exact code you've written (without any modifications), it works. Note that I just changed summarize to summarise to test it out.
The function works as expected. I'm not sure why, but thought I'd report it as an issue.
My session info: