First of all, thanks for your excellent work. I have learned a lot of skills here.
I can reproduce all results with demo datasets. However, When I repeat it with my own data, some error occured as following:
library(structToolbox)
load("test.Rdata")
mD <- DatasetExperiment(name = "mD",
data = mconc,
sample_meta = mmeta,
variable_meta = data.frame(variable = colnames(mconc),row.names = colnames(mconc) ) ,
description = "The test"
)
mD$sample_meta$FN <- as.factor(mD$sample_meta$FN)
P = PLSDA(number_components = 2, factor_name= "FN" )
# apply the model
P = model_apply(P,mD)
C = pls_scores_plot(components=c(1,2),factor_name = "FN" )
chart_plot(C,P)
# prepare chart
C = pls_vip_plot(ycol = 'HE')
g1 = chart_plot(C,P)
Error in `$<-.data.frame`(`*tmp*`, "feature", value = c("pos.M68T423", :
replacement has 1000 rows, data has 0
6.
stop(sprintf(ngettext(N, "replacement has %d row, data has %d",
"replacement has %d rows, data has %d"), N, nrows), domain = NA)
5.
`$<-.data.frame`(`*tmp*`, "feature", value = c("pos.M68T423",
"pos.M69T424", "pos.M70T363", "pos.M70T442", "pos.M70T535", "pos.M70T258",
"pos.M71T363", "pos.M72T349", "pos.M73T351", "pos.M74T449", "pos.M74T415",
"pos.M74T57", "pos.M74T129", "pos.M74T403", "pos.M74T602", "pos.M75T415", ...
4.
`$<-`(`*tmp*`, "feature", value = c("pos.M68T423", "pos.M69T424",
"pos.M70T363", "pos.M70T442", "pos.M70T535", "pos.M70T258", "pos.M71T363",
"pos.M72T349", "pos.M73T351", "pos.M74T449", "pos.M74T415", "pos.M74T57",
"pos.M74T129", "pos.M74T403", "pos.M74T602", "pos.M75T415", "pos.M76T415", ...
3.
.local(obj, dobj, ...)
2.
chart_plot(C, P)
1.
chart_plot(C, P)
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.4.2.1 xlsx_0.6.5 pmp_1.14.0 BiocFileCache_2.10.1 dbplyr_2.4.0 cowplot_1.1.1 structToolbox_1.14.0 struct_1.14.0 lubridate_1.9.3
[10] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0
[19] omu_1.1.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 magrittr_2.0.3 farver_2.1.1 zlibbioc_1.48.0 vctrs_0.6.4 memoise_2.0.1
[7] RCurl_1.98-1.13 rstatix_0.7.2 S4Arrays_1.2.0 itertools_0.1-3 missForest_1.5 curl_5.1.0
[13] broom_1.0.5 SparseArray_1.2.2 pROC_1.18.5 caret_6.0-94 FSA_0.9.5 parallelly_1.36.0
[19] desc_1.4.2 plyr_1.8.9 impute_1.76.0 cachem_1.0.8 lifecycle_1.0.4 iterators_1.0.14
[25] pkgconfig_2.0.3 Matrix_1.6-3 R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[31] future_1.33.0 digest_0.6.33 pcaMethods_1.94.0 colorspace_2.1-0 ps_1.7.5 S4Vectors_0.40.1
[37] rprojroot_2.0.4 GenomicRanges_1.54.1 RSQLite_2.3.3 filelock_1.0.2 labeling_0.4.3 randomForest_4.7-1.1
[43] fansi_1.0.5 timechange_0.2.0 httr_1.4.7 abind_1.4-5 compiler_4.3.2 rngtools_1.5.2
[49] bit64_4.0.5 withr_2.5.2 backports_1.4.1 carData_3.0-5 DBI_1.1.3 pkgbuild_1.4.2
[55] MASS_7.3-60 lava_1.7.3 DelayedArray_0.28.0 ModelMetrics_1.2.2.2 tools_4.3.2 future.apply_1.11.0
[61] nnet_7.3-19 glue_1.6.2 callr_3.7.3 nlme_3.1-163 grid_4.3.2 reshape2_1.4.4
[67] generics_0.1.3 recipes_1.0.8 gtable_0.3.4 tzdb_0.4.0 class_7.3-22 data.table_1.14.8
[73] hms_1.1.3 sp_2.1-1 car_3.1-2 utf8_1.2.4 XVector_0.42.0 BiocGenerics_0.48.1
[79] foreach_1.5.2 pillar_1.9.0 rJava_1.0-6 splines_4.3.2 lattice_0.22-5 survival_3.5-7
[85] bit_4.0.5 tidyselect_1.2.0 knitr_1.45 gridExtra_2.3 IRanges_2.36.0 SummarizedExperiment_1.32.0
[91] stats4_4.3.2 xfun_0.41 pls_2.8-3 Biobase_2.62.0 hardhat_1.3.0 timeDate_4022.108
[97] matrixStats_1.1.0 stringi_1.8.1 xlsxjars_0.6.1 codetools_0.2-19 BiocManager_1.30.22 cli_3.6.1
[103] ontologyIndex_2.11 rpart_4.1.21 processx_3.8.2 munsell_0.5.0 Rcpp_1.0.11 GenomeInfoDb_1.38.1
[109] globals_0.16.2 parallel_4.3.2 ggfortify_0.4.16 gower_1.0.1 blob_1.2.4 prettyunits_1.2.0
[115] doRNG_1.8.6 bitops_1.0-7 listenv_0.9.0 ggthemes_4.2.4 viridisLite_0.4.2 ipred_0.9-14
[121] scales_1.2.1 prodlim_2023.08.28 crayon_1.5.2 rlang_1.1.2
First of all, thanks for your excellent work. I have learned a lot of skills here.
I can reproduce all results with demo datasets. However, When I repeat it with my own data, some error occured as following:
test.zip
the Erroe message like this:
my R evironment ：