Comments (8)
Hello, I've done the updates required by the new OMA API. If you update OmnipathR
from github, I expect it should work:
remotes::install_github('saezlab/OmnipathR')
from omnipathr.
Hello, Could you please share a full trace (by traceback
, or by rlang::last_trace
), and also the output of sessionInfo()
?
from omnipathr.
from omnipathr.
> library(decoupleR)
> library(dplyr)
> library(tibble)
> library(tidyr)
> library(ggplot2)
> library(pheatmap)
> library(ggrepel)
> net <- get_progeny(organism = 'human', top = 500)
[2024-04-24 01:26:29] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
> net <- get_progeny(organism = 'mouse', top = 500)
[2024-04-24 01:26:46] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggrepel_0.9.5 pheatmap_1.0.12 ggplot2_3.5.0 tidyr_1.3.1 tibble_3.2.1
[6] dplyr_1.1.4 decoupleR_2.9.7
loaded via a namespace (and not attached):
[1] logger_0.3.0 readxl_1.4.3 rlang_1.1.3
[4] magrittr_2.0.3 compiler_4.3.1 systemfonts_1.0.5
[7] vctrs_0.6.5 devEMF_4.4-2 rvest_1.0.4
[10] stringr_1.5.1 httpcode_0.3.0 pkgconfig_2.0.3
[13] crayon_1.5.2 fastmap_1.1.1 backports_1.4.1
[16] ellipsis_0.3.2 utf8_1.2.4 promises_1.2.1
[19] rmarkdown_2.26 tzdb_0.4.0 ragg_1.2.7
[22] bit_4.0.5 purrr_1.0.2 xfun_0.43
[25] jsonlite_1.8.8 progress_1.2.3 later_1.3.2
[28] uuid_1.2-0 BiocParallel_1.34.2 tweenr_2.0.2
[31] broom_1.0.5 parallel_4.3.1 prettyunits_1.2.0
[34] R6_2.5.1 stringi_1.8.3 RColorBrewer_1.1-3
[37] parallelly_1.37.0 lubridate_1.9.3 cellranger_1.1.0
[40] Rcpp_1.0.12 knitr_1.46 base64enc_0.1-3
[43] readr_2.1.5 httpuv_1.6.14 Matrix_1.6-5
[46] igraph_2.0.3 timechange_0.3.0 tidyselect_1.2.1
[49] rstudioapi_0.15.0 yaml_2.3.8 codetools_0.2-19
[52] curl_5.2.0 lattice_0.22-5 shiny_1.8.0
[55] withr_3.0.0 flextable_0.9.4 askpass_1.2.0
[58] evaluate_0.23 polyclip_1.10-6 zip_2.3.1
[61] stargazer_5.2.3 xml2_1.3.6 pillar_1.9.0
[64] checkmate_2.3.1 generics_0.1.3 vroom_1.6.5
[67] hms_1.1.3 munsell_0.5.1 scales_1.3.0
[70] xtable_1.8-4 OmnipathR_3.10.1 glue_1.7.0
[73] gdtools_0.3.6 tools_4.3.1 gfonts_0.2.0
[76] data.table_1.15.0 openxlsx_4.2.5.2 rgl_1.2.8
[79] cowplot_1.1.3 grid_4.3.1 colorspace_2.1-0
[82] export_0.3.0 ggforce_0.4.2 cli_3.6.2
[85] rappdirs_0.3.3 rvg_0.3.3 textshaping_0.3.7
[88] officer_0.6.5 fontBitstreamVera_0.1.1 fansi_1.0.6
[91] gtable_0.3.4 selectr_0.4-2 digest_0.6.34
[94] fontquiver_0.2.1 crul_1.4.0 htmlwidgets_1.6.4
[97] farver_2.1.1 htmltools_0.5.7 lifecycle_1.0.4
[100] httr_1.4.7 mime_0.12 bit64_4.0.5
[103] fontLiberation_0.1.0 openssl_2.1.1 MASS_7.3-60.0.1
> traceback
function (x = NULL, max.lines = getOption("traceback.max.lines",
getOption("deparse.max.lines", -1L)))
{
n <- length(x <- .traceback(x, max.lines = max.lines))
if (n == 0L)
cat(gettext("No traceback available"), "\n")
else {
for (i in 1L:n) {
xi <- x[[i]]
label <- paste0(n - i + 1L, ": ")
m <- length(xi)
srcloc <- if (!is.null(srcref <- attr(xi, "srcref"))) {
srcfile <- attr(srcref, "srcfile")
paste0(" at ", basename(srcfile$filename), "#",
srcref[1L])
}
if (isTRUE(attr(xi, "truncated"))) {
xi <- c(xi, " ...")
m <- length(xi)
}
if (!is.null(srcloc)) {
xi[m] <- paste0(xi[m], srcloc)
}
if (m > 1)
label <- c(label, rep(substr(" ", 1L,
nchar(label, type = "w")), m - 1L))
cat(paste0(label, xi), sep = "\n")
}
}
invisible(x)
}
<bytecode: 0x0000024a8f63f2a8>
<environment: namespace:base>
from omnipathr.
"human" can run successfully, but "mouse" will error
Thank you
from omnipathr.
Thanks! Above you pasted the code of the traceback
function, you have to call it: traceback()
. Also, before checking again, I'd recommend to update OmnipathR
from git:
remotes::install_github('saezlab/OmnipathR')
from omnipathr.
I am so sorry, I have updated "OmnipathR" according to your suggestion. Unfortunately, it shows the same error.
> traceback()
29: mutate(., across(starts_with("id_organism"), ~str_extract(.x,
"([^_]*)")))
28: filter(., !str_detect(id_organism_a, sprintf("%s\\d+", organism_a)) &
!str_detect(id_organism_b, sprintf("%s\\d+", organism_b)) &
mapping %in% mappings)
27: "oma_pairwise" %>% generic_downloader(reader_param = list(col_names = c("id_organism_a",
"id_organism_b", "mapping", "oma_group"), col_types = cols(),
comment = "#"), url_param = list(organism_a, organism_b,
id_type)) %>% mutate(across(starts_with("id_organism"), ~str_extract(.x,
"([^_]*)"))) %>% filter(!str_detect(id_organism_a, sprintf("%s\\d+",
organism_a)) & !str_detect(id_organism_b, sprintf("%s\\d+",
organism_b)) & mapping %in% mappings) %>% {
if (only_ids)
select(., id_organism_a, id_organism_b)
else .
}
26: (function (organism_a = "human", organism_b = "mouse", id_type = "uniprot",
mappings = c("1:1", "1:m", "n:1", "n:m"), only_ids = TRUE)
{
.slow_doctest()
if (id_type == "genesymbol") {
id_type <- "uniprot"
return(environment() %>% as.list %>% exec(oma_pairwise_genesymbols,
!!!.))
}
id_organism_a <- id_organism_b <- mapping <- NULL
organism_a %<>% oma_code
organism_b %<>% oma_code
id_type %<>% oma_id_type
args <- match.call() %>% as.list %>% tail(-1L)
for (arg in names(args)) {
if (is.null(get(arg)) || any(is.na(get(arg)))) {
msg <- sprintf("Could not recognize %s: `%s`.", if (arg ==
"id_type")
"ID type"
else "organism", args[[arg]])
...
25: exec(loader, !!!param)
24: load_db(key, param = param)
23: get_db(db_name, param = orthology_param)
22: select(., -any_of("hgroup"))
21: set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
20: get_db(db_name, param = orthology_param) %>% select(-any_of("hgroup")) %>%
set_names(c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL)) %>% {
if (translate_complexes)
bind_rows(., complex_orthology(orthology = ., identifiers = data %>%
pull(!!sym(column)), one_to_many = translate_complexes))
else .
}
19: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism,
replace = TRUE)
18: OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
17: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism,
replace = TRUE) %>% OmnipathR::translate_ids(., uniprot,
genesymbol, organism = organism)
16: tryCatch(OmnipathR::import_omnipath_annotations(resources = name,
..., wide = TRUE), error = function(e) {
tryCatch(OmnipathR::static_table(query = "annotations", resource = name,
organism = organism), error = function(e) {
msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ",
"from OmniPath. For more information, see the OmnipathR log."),
name)
OmnipathR::omnipath_msg("error", msg)
stop(msg)
})
}) %>% {
if (organism != 9606L)
OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism,
replace = TRUE) %>% OmnipathR::translate_ids(., uniprot,
genesymbol, organism = organism)
else .
}
15: get_resource("PROGENy", organism = organism)
14: dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
13: dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
12: dplyr::select(., genesymbol, p_value, pathway, weight)
11: dplyr::group_by(., pathway)
10: dplyr::group_split(.)
9: vctrs_vec_compat(.x, .purrr_user_env)
8: map_("list", .x, .f, ..., .progress = .progress)
7: purrr::map(., function(df) {
df %>% dplyr::arrange(p_value) %>% head(top)
})
6: list2(...)
5: dplyr::bind_rows(.)
4: dplyr::select(., pathway, genesymbol, weight, p_value)
3: rlang::set_names(., c("source", "target", "weight", "p_value"))
2: get_resource("PROGENy", organism = organism) %>% dplyr::distinct(pathway,
genesymbol, .keep_all = TRUE) %>% dplyr::mutate(weight = as.double(weight),
p_value = as.double(p_value)) %>% dplyr::select(genesymbol,
p_value, pathway, weight) %>% dplyr::group_by(pathway) %>%
dplyr::group_split() %>% purrr::map(function(df) {
df %>% dplyr::arrange(p_value) %>% head(top)
}) %>% dplyr::bind_rows() %>% dplyr::select(pathway, genesymbol,
weight, p_value) %>% rlang::set_names(c("source", "target",
"weight", "p_value"))
1: get_progeny(organism = "mouse", top = 500)
from omnipathr.
Thanks for the traceback, I found that OMA, the resource that we use for gene orthology data, has updated its HTTP API very recently. Hence I have to do some updates in OmnipathR
, adjusting it to the new API. I'll do this most likely tomorrow, and let you know here once ready. Thank you for reporting this issue!
from omnipathr.
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