Output html processing information
Xiaotao Shen
Created on 2021-12-04 and updated on 2026-03-02
Source:vignettes/html_process_info.Rmd
html_process_info.RmdIntroduction
We can output the process_info into a html format file,
so we can know what processing steps have been made to this object and
the accurate parameters.
report_parameters()
library(massdataset)
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)
library(tidyverse)
object =
object %>%
activate_mass_dataset(what = "expression_data") %>%
filter(!is.na(QC_1))
object =
object %>%
activate_mass_dataset(what = "expression_data") %>%
filter(!is.na(QC_2))
object =
object %>%
mutate_mean_intensity()
object =
object %>%
mutate_median_intensity() %>%
mutate_rsd()
object@process_info
#> $create_mass_dataset
#> --------------------
#> pacakge_name: massdataset
#> function_name: create_mass_dataset()
#> time: 2026-03-02 09:28:07.344076
#> parameters:
#> no : no
#>
#> $filter
#> $filter[[1]]
#> --------------------
#> pacakge_name: massdataset
#> function_name: filter()
#> time: 2026-03-02 09:28:07.470212
#> parameters:
#> parameter : `~!is.na(QC_1)`
#>
#> $filter[[2]]
#> --------------------
#> pacakge_name: massdataset
#> function_name: filter()
#> time: 2026-03-02 09:28:07.471133
#> parameters:
#> parameter : `~!is.na(QC_2)`
#>
#>
#> $mutate_mean_intensity
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_mean_intensity()
#> time: 2026-03-02 09:28:07.47368
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")
#>
#> $mutate_median_intensity
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_median_intensity()
#> time: 2026-03-02 09:28:07.480952
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")
#>
#> $mutate_rsd
#> --------------------
#> pacakge_name: massdataset
#> function_name: mutate_rsd()
#> time: 2026-03-02 09:28:07.4849
#> parameters:
#> according_to_samples : c("Blank_3", "Blank_4", "QC_1", "QC_2", "PS4P1", "PS4P2", "PS4P3", "PS4P4")Then we can use report_parameters() to output this into
a html file.
report_parameters(object = object, path = "demo_data")A html file named as parameter_report.html will be
placed in ./demo_data.
Example HTML parameter report generated from
process_info.
Session information
sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Tahoe 26.3
#>
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
#>
#> locale:
#> [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
#>
#> time zone: Asia/Singapore
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 purrr_1.1.0
#> [5] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 tidyverse_2.0.0
#> [9] magrittr_2.0.3 dplyr_1.1.4 ggplot2_4.0.2 massdataset_0.99.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.1 farver_2.1.2
#> [3] S7_0.2.0 fastmap_1.2.0
#> [5] digest_0.6.37 timechange_0.3.0
#> [7] lifecycle_1.0.4 cluster_2.1.8.1
#> [9] compiler_4.5.2 rlang_1.1.6
#> [11] sass_0.4.10 tools_4.5.2
#> [13] yaml_2.3.10 knitr_1.50
#> [15] S4Arrays_1.8.1 htmlwidgets_1.6.4
#> [17] DelayedArray_0.34.1 RColorBrewer_1.1-3
#> [19] abind_1.4-8 withr_3.0.2
#> [21] BiocGenerics_0.54.0 desc_1.4.3
#> [23] grid_4.5.2 stats4_4.5.2
#> [25] colorspace_2.1-1 scales_1.4.0
#> [27] iterators_1.0.14 dichromat_2.0-0.1
#> [29] SummarizedExperiment_1.38.1 cli_3.6.5
#> [31] rmarkdown_2.29 crayon_1.5.3
#> [33] ragg_1.4.0 generics_0.1.4
#> [35] rstudioapi_0.17.1 httr_1.4.7
#> [37] tzdb_0.5.0 rjson_0.2.23
#> [39] cachem_1.1.0 parallel_4.5.2
#> [41] XVector_0.48.0 matrixStats_1.5.0
#> [43] vctrs_0.6.5 Matrix_1.7-4
#> [45] jsonlite_2.0.0 IRanges_2.42.0
#> [47] hms_1.1.3 GetoptLong_1.0.5
#> [49] S4Vectors_0.48.0 clue_0.3-66
#> [51] systemfonts_1.2.3 foreach_1.5.2
#> [53] jquerylib_0.1.4 glue_1.8.0
#> [55] pkgdown_2.1.3 codetools_0.2-20
#> [57] stringi_1.8.7 shape_1.4.6.1
#> [59] gtable_0.3.6 GenomeInfoDb_1.44.2
#> [61] GenomicRanges_1.60.0 UCSC.utils_1.4.0
#> [63] ComplexHeatmap_2.24.1 pillar_1.11.0
#> [65] htmltools_0.5.8.1 GenomeInfoDbData_1.2.14
#> [67] circlize_0.4.16 R6_2.6.1
#> [69] textshaping_1.0.1 doParallel_1.0.17
#> [71] evaluate_1.0.4 Biobase_2.68.0
#> [73] lattice_0.22-7 png_0.1-8
#> [75] openxlsx_4.2.8 bslib_0.9.0
#> [77] Rcpp_1.1.0 zip_2.3.3
#> [79] SparseArray_1.8.1 xfun_0.53
#> [81] fs_1.6.6 MatrixGenerics_1.20.0
#> [83] pkgconfig_2.0.3 GlobalOptions_0.1.2