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README update
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‎README.md‎

Lines changed: 33 additions & 56 deletions
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@@ -66,26 +66,15 @@ The standard SummarizedExperiment display:
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``` r
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airway
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#> # A SummarizedExperiment-tibble abstraction: Features=63677 | Samples=8 |
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#> # Assays=counts
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#> # |----------------- COVARIATES ---------------|
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#> .feature .sample | counts | SampleName cell dex albut Run avgLength
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#> <chr> <chr> | <chr> | <fct> <fct> <fct> <fct> <fct> <chr>
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#> 1 ENSG0000… SRR103… | 679 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 2 ENSG0000… SRR103… | 0 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 3 ENSG0000… SRR103… | 467 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 4 ENSG0000… SRR103… | 260 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 5 ENSG0000… SRR103… | 60 | GSM1275862 N613… untrt untrt SRR1… 126
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#> -------- ------- - ------ - ---------- ---- --- ----- --- ---------
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#> 509412 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509413 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509414 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509415 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509416 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> # ℹ 14 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>,
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#> # `|` <|>, gene_id <chr>, gene_name <chr>, entrezid <chr>,
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#> # gene_biotype <chr>, gene_seq_start <chr>, gene_seq_end <chr>,
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#> # seq_name <chr>, seq_strand <chr>, seq_coord_system <chr>, symbol <chr>
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#> class: RangedSummarizedExperiment
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#> dim: 63677 8
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#> metadata(1): ''
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#> assays(1): counts
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#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
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#> ENSG00000273493
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#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
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#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
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#> colData names(9): SampleName cell ... Sample BioSample
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```
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### **tidyprint**
@@ -95,26 +84,15 @@ Now we load tidyprint for a tidy data display
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``` r
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library(tidyprint)
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airway
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#> # A SummarizedExperiment-tibble abstraction: Features=63677 | Samples=8 |
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#> # Assays=counts
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#> # |----------------- COVARIATES ---------------|
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#> .feature .sample | counts | SampleName cell dex albut Run avgLength
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#> <chr> <chr> | <chr> | <fct> <fct> <fct> <fct> <fct> <chr>
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#> 1 ENSG0000… SRR103… | 679 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 2 ENSG0000… SRR103… | 0 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 3 ENSG0000… SRR103… | 467 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 4 ENSG0000… SRR103… | 260 | GSM1275862 N613… untrt untrt SRR1… 126
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#> 5 ENSG0000… SRR103… | 60 | GSM1275862 N613… untrt untrt SRR1… 126
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#> -------- ------- - ------ - ---------- ---- --- ----- --- ---------
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#> 509412 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509413 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509414 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509415 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> 509416 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
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#> # ℹ 14 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>,
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#> # `|` <|>, gene_id <chr>, gene_name <chr>, entrezid <chr>,
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#> # gene_biotype <chr>, gene_seq_start <chr>, gene_seq_end <chr>,
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#> # seq_name <chr>, seq_strand <chr>, seq_coord_system <chr>, symbol <chr>
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#> class: RangedSummarizedExperiment
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#> dim: 63677 8
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#> metadata(1): ''
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#> assays(1): counts
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#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
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#> ENSG00000273493
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#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
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#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
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#> colData names(9): SampleName cell ... Sample BioSample
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```
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------------------------------------------------------------------------
@@ -255,20 +233,19 @@ sessionInfo()
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#> [13] dplyr_1.1.4
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#>
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#> loaded via a namespace (and not attached):
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#> [1] utf8_1.2.6 sass_0.4.10 generics_0.1.4
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#> [4] SparseArray_1.6.2 stringi_1.8.7 lattice_0.22-7
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#> [7] digest_0.6.37 magrittr_2.0.3 evaluate_1.0.4
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#> [10] grid_4.4.0 fastmap_1.2.0 rprojroot_2.1.0
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#> [13] jsonlite_2.0.0 Matrix_1.7-3 httr_1.4.7
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#> [16] fansi_1.0.6 purrr_1.1.0 UCSC.utils_1.2.0
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#> [19] jquerylib_0.1.4 abind_1.4-8 cli_3.6.5
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#> [22] rlang_1.1.6 crayon_1.5.3 XVector_0.46.0
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#> [25] withr_3.0.2 cachem_1.1.0 DelayedArray_0.32.0
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#> [28] yaml_2.3.10 S4Arrays_1.6.0 tools_4.4.0
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#> [31] GenomeInfoDbData_1.2.13 vctrs_0.6.5 R6_2.6.1
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#> [34] lifecycle_1.0.4 stringr_1.5.1 zlibbioc_1.52.0
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#> [37] pkgconfig_2.0.3 pillar_1.11.0 bslib_0.9.0
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#> [40] glue_1.8.0 xfun_0.52 tibble_3.3.0
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#> [43] tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.50
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#> [46] htmltools_0.5.8.1 rmarkdown_2.29 compiler_4.4.0
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#> [1] utf8_1.2.6 generics_0.1.4 SparseArray_1.6.2
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#> [4] stringi_1.8.7 lattice_0.22-7 digest_0.6.37
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#> [7] magrittr_2.0.3 evaluate_1.0.4 grid_4.4.0
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#> [10] fastmap_1.2.0 rprojroot_2.1.0 jsonlite_2.0.0
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#> [13] Matrix_1.7-3 httr_1.4.7 fansi_1.0.6
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#> [16] purrr_1.1.0 UCSC.utils_1.2.0 abind_1.4-8
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#> [19] cli_3.6.5 rlang_1.1.6 crayon_1.5.3
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#> [22] XVector_0.46.0 withr_3.0.2 DelayedArray_0.32.0
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#> [25] yaml_2.3.10 S4Arrays_1.6.0 tools_4.4.0
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#> [28] GenomeInfoDbData_1.2.13 vctrs_0.6.5 R6_2.6.1
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#> [31] lifecycle_1.0.4 stringr_1.5.1 zlibbioc_1.52.0
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#> [34] pkgconfig_2.0.3 pillar_1.11.0 glue_1.8.0
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#> [37] xfun_0.52 tibble_3.3.0 tidyselect_1.2.1
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#> [40] rstudioapi_0.17.1 knitr_1.50 htmltools_0.5.8.1
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#> [43] rmarkdown_2.29 compiler_4.4.0
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```

‎vignettes/Introduction.Rmd‎

Lines changed: 8 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -11,20 +11,18 @@ knit: >
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(function(x, ...){
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proj_root <- rprojroot::find_package_root_file() |> normalizePath()
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rmarkdown::render(
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x,
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output_format = "html_document",
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params = list(
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demo_metadata = TRUE
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)
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x,
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output_file = "README.md",
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output_format = "github_document",
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output_dir = proj_root,
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knit_root_dir = proj_root,
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params = list( demo_metadata = FALSE )
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)
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rmarkdown::render(
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x,
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output_file = "README.md",
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output_format = "github_document",
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output_dir = proj_root,
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knit_root_dir = proj_root,
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output_format = "html_document",
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params = list(
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demo_metadata = FALSE
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demo_metadata = TRUE
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)
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)
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})

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