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canrep: explicit namespaces
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@pdiakumis
pdiakumis committed May 7, 2024
1 parent eae65f5 commit 3dab6c8
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Showing 3 changed files with 43 additions and 46 deletions.
2 changes: 1 addition & 1 deletion R/oncokb.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
#' @return Vector of genes.
#' @export
read_oncokb <- function(x) {
readr::read_tsv(x) |>
readr::read_tsv(x, col_types = readr::cols(.default = "c")) |>
dplyr::filter(
.data$`OncoKB Annotated` == "Yes"
) |>
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78 changes: 38 additions & 40 deletions inst/rmd/umccrise/cancer_report.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -48,30 +48,30 @@ knitr::opts_chunk$set(

```{r load_pkgs}
# Bioconductor
library(BSgenome)
library(MutationalPatterns)
library(BSgenome, include.only = "BSgenome")
library(MutationalPatterns, include.only = "read_vcfs_as_granges")
ref_genome <- "BSgenome.Hsapiens.UCSC.hg38"
library(ref_genome, character.only = TRUE)
library(ref_genome, character.only = TRUE, include.only = ref_genome)
tx_ref_genome <- "TxDb.Hsapiens.UCSC.hg38.knownGene"
library(tx_ref_genome, character.only = TRUE)
library(tx_ref_genome, character.only = TRUE, include.only = tx_ref_genome)
# CRAN
library(devtools)
library(details)
library(DT)
library(details, include.only = "details")
library(DT, include.only = "datatable")
library(dplyr)
library(glue)
library(gt)
library(ggplot2)
library(htmltools)
library(jsonlite)
library(GenomeInfoDb, include.only = "seqlevelsStyle")
library(GenomicFeatures, include.only = "genes")
library(GenomicRanges, include.only = "GRanges")
library(glue, include.only = "glue")
library(gt, include.only = "gt")
library(ggplot2, include.only = "ggtitle")
library(IRanges, include.only = "IRanges")
library(knitr)
library(kableExtra)
library(kableExtra, include.only = "kable_styling")
library(patchwork)
library(purrr)
library(readr)
library(rmarkdown)
library(stringr)
library(tidyr)
library(purrr, include.only = "map")
library(readr, include.only = "read_tsv")
library(rmarkdown, include.only = "render")
library(tidyr, include.only = "pivot_longer")
# umccr
library(gpgr)
library(sigrap)
Expand Down Expand Up @@ -388,50 +388,50 @@ qc_summary_all %>%
gt::gt(rowname_col = "variable") %>%
gt::tab_style(
style = list(
cell_fill(color = red),
cell_text(weight = "bold")
gt::cell_fill(color = red),
gt::cell_text(weight = "bold")
),
locations = cells_body(
locations = gt::cells_body(
columns = value,
rows = grepl("FAIL", value) & variable == "QC_Status"
)
) %>%
gt::tab_style(
style = list(
cell_fill(color = orange),
cell_text(weight = "bold")
gt::cell_fill(color = orange),
gt::cell_text(weight = "bold")
),
locations = cells_body(
locations = gt::cells_body(
columns = value,
rows = grepl("WARN_", value) & variable == "QC_Status"
)
) %>%
gt::tab_style(
style = list(
cell_fill(color = orange),
cell_text(weight = "bold")
gt::cell_fill(color = orange),
gt::cell_text(weight = "bold")
),
locations = cells_body(
locations = gt::cells_body(
columns = value,
rows = grepl("TRUE", value) & variable == "Hypermutated"
)
) %>%
gt::tab_style(
style = list(
cell_text(weight = "bold")
gt::cell_text(weight = "bold")
),
locations = list(
cells_stub(rows = TRUE),
cells_body(columns = value)
gt::cells_stub(rows = TRUE),
gt::cells_body(columns = value)
)
) %>%
gt::cols_align("left") %>%
# align rowname_col
gt::tab_style(
style = list(
cell_text(align = "left")
gt::cell_text(align = "left")
),
locations = cells_stub(rows = TRUE)
locations = gt::cells_stub(rows = TRUE)
) %>%
gt::opt_row_striping() %>%
gt::tab_options(table.align = "left")
Expand Down Expand Up @@ -560,7 +560,6 @@ mp_plot_bias2 <- MutationalPatterns::plot_strand_bias(strand_bias)
## ---- Replicative ---- ##
repli_file <- system.file("extdata/ReplicationDirectionRegions.bed",
package = "MutationalPatterns"
)
Expand Down Expand Up @@ -1012,9 +1011,9 @@ d %>%
gt::sub_missing(columns = dplyr::everything()) %>%
gt::tab_style(
style = list(
cell_text(weight = "bold")
gt::cell_text(weight = "bold")
),
locations = cells_stub(rows = TRUE)
locations = gt::cells_stub(rows = TRUE)
) %>%
gt::cols_align("right") %>%
gt::tab_options(table.align = "left")
Expand Down Expand Up @@ -1135,7 +1134,7 @@ purple_cnv_som_gene$descr %>%
dplyr::mutate(
Column = kableExtra::cell_spec(Column, bold = TRUE)
) %>%
knitr::kable(escape = FALSE) %>%
kableExtra::kbl(escape = FALSE) %>%
kableExtra::kable_paper(c("hover", "striped"), full_width = FALSE, position = "left") %>%
kableExtra::scroll_box(height = "200px")
```
Expand Down Expand Up @@ -1178,7 +1177,7 @@ purple_cnv_som$descr %>%
dplyr::mutate(
Column = kableExtra::cell_spec(Column, bold = TRUE)
) %>%
knitr::kable(escape = FALSE) %>%
kableExtra::kbl(escape = FALSE) %>%
kableExtra::kable_paper(c("hover", "striped"), full_width = FALSE, position = "left") %>%
kableExtra::scroll_box(height = "200px")
```
Expand Down Expand Up @@ -1371,7 +1370,7 @@ if (is.null(params$conda_list)) {
)
) %>%
dplyr::left_join(conda_pkgs, by = "name") %>%
knitr::kable(format = "html") %>%
kableExtra::kbl() %>%
kableExtra::kable_paper(c("hover", "striped"), full_width = TRUE, position = "left") %>%
kableExtra::column_spec(1, bold = TRUE) %>%
kableExtra::scroll_box(height = "300px")
Expand All @@ -1383,9 +1382,8 @@ if (is.null(params$conda_list)) {
```{r report_inputs}
report_inputs <- dplyr::tibble(key = names(params), value = params)
gpgr::write_tsvjsongz(report_inputs, glue("{bnm}-report_inputs"), result_outdir)
report_inputs %>%
knitr::kable(format = "html") %>%
kableExtra::kbl() %>%
kableExtra::kable_paper(c("hover", "striped"), full_width = FALSE, position = "left") %>%
kableExtra::column_spec(1, bold = TRUE) %>%
kableExtra::scroll_box(height = "200px")
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9 changes: 4 additions & 5 deletions inst/rmd/umccrise/render.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,7 @@ require(purrr)

batch_name <- "SBJ00480_PTC_HCC1395t100pc"
tumor_name <- "PTC_HCC1395t100pc"
umccrised_dir <- here("nogit/umccrised_data/seqc_inputs.20231115")

umccrised_dir <- here::here("nogit/umccrised_data/seqc_inputs.20231115")
params <- list(
af_global = glue("{umccrised_dir}/sample_data/af_tumor.txt"),
af_keygenes = glue("{umccrised_dir}/sample_data/af_tumor_keygenes.txt"),
Expand All @@ -17,7 +16,7 @@ params <- list(
conda_list = NULL,
dragen_hrd = glue("{umccrised_dir}/sample_data/{tumor_name}.hrdscore.csv"),
img_dir = glue("{umccrised_dir}/output/img"),
key_genes = glue("{umccrised_dir}/reference_data/umccr_cancer_genes.latest.tsv"),
key_genes = normalizePath("./inst/extdata/ref/umccr_cancer_genes_v24.03.0.tsv"),
oncokb_genes = glue("{umccrised_dir}/reference_data/oncokb_genes.20231113.tsv"),
virusbreakend_tsv = glue("{umccrised_dir}/sample_data/virusbreakend/{batch_name}.virusbreakend.vcf.summary.tsv"),
virusbreakend_vcf = glue("{umccrised_dir}/sample_data/virusbreakend/{batch_name}.virusbreakend.vcf"),
Expand All @@ -30,8 +29,8 @@ params <- list(
result_outdir = glue("{umccrised_dir}/output/cancer_report_tables"),
somatic_snv_vcf = glue("{umccrised_dir}/sample_data/{tumor_name}.pass.vcf.gz"),
somatic_snv_summary = glue("{umccrised_dir}/sample_data/{tumor_name}.somatic.variant_counts_process.json"),
somatic_sv_tsv = glue("{umccrised_dir}/sample_data/{tumor_name}.sv.prioritised.tsv"),
somatic_sv_vcf = glue("{umccrised_dir}/sample_data/{tumor_name}.sv.prioritised.vcf.gz"),
somatic_sv_tsv = here::here("inst/extdata/sash/sv.prioritised.tsv"),
somatic_sv_vcf = here::here("inst/extdata/sash/sv.prioritised.vcf.gz"),
tumor_name = tumor_name
)

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