Commit b4e2ed9e authored by Pradat Yoann's avatar Pradat Yoann

update pcawg_count data docs

parent 0031e711
......@@ -19,6 +19,9 @@ check:
image: gitlab-research.centralesupelec.fr:4567/2019pradaty/tableextra_docker
script:
- Rscript -e 'if (!identical(devtools::check(document = FALSE, args = "--no-tests")[["errors"]], character(0))) stop("Check with Errors")'
only:
refs:
- master
test:
stage: test
......@@ -26,6 +29,9 @@ test:
script:
- Rscript -e 'if (any(as.data.frame(devtools::test())[["failed"]] > 0)) stop("Some tests failed.")'
- Rscript -e 'covr::codecov()'
only:
refs:
- master
install:
stage: check
......@@ -33,3 +39,6 @@ install:
script:
- Rscript -e 'devtools::build(binary=T)'
- Rscript -e 'devtools::install()'
only:
refs:
- master
......@@ -13,7 +13,70 @@
#' \item{Sample.Names}{Unique tumour identifiers}
#' \item{Accuracy}{Cosine similarity between the tumour's mutational profile and the reconstructed mutational profile}
#' \item{SBS1}{Single-base-substitution signature 1. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS1.tt>}
#' ...
#' \item{SBS10a}{Single-base-substitution signature 10a. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS10a.tt>}
#' \item{SBS10b}{Single-base-substitution signature 10b. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS10b.tt>}
#' \item{SBS11}{Single-base-substitution signature 11. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS11.tt>}
#' \item{SBS12}{Single-base-substitution signature 12. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS12.tt>}
#' \item{SBS13}{Single-base-substitution signature 13. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS13.tt>}
#' \item{SBS14}{Single-base-substitution signature 14. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS14.tt>}
#' \item{SBS15}{Single-base-substitution signature 15. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS15.tt>}
#' \item{SBS16}{Single-base-substitution signature 16. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS16.tt>}
#' \item{SBS17a}{Single-base-substitution signature 17a. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS17a.tt>}
#' \item{SBS17b}{Single-base-substitution signature 17b. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS17b.tt>}
#' \item{SBS18}{Single-base-substitution signature 18. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS18.tt>}
#' \item{SBS19}{Single-base-substitution signature 19. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS19.tt>}
#' \item{SBS20}{Single-base-substitution signature 20. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS20.tt>}
#' \item{SBS2}{Single-base-substitution signature 2. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS2.tt>}
#' \item{SBS21}{Single-base-substitution signature 21. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS21.tt>}
#' \item{SBS22}{Single-base-substitution signature 22. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS22.tt>}
#' \item{SBS23}{Single-base-substitution signature 23. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS23.tt>}
#' \item{SBS24}{Single-base-substitution signature 24. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS24.tt>}
#' \item{SBS25}{Single-base-substitution signature 25. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS25.tt>}
#' \item{SBS26}{Single-base-substitution signature 26. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS26.tt>}
#' \item{SBS27}{Single-base-substitution signature 27. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS27.tt>}
#' \item{SBS28}{Single-base-substitution signature 28. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS28.tt>}
#' \item{SBS29}{Single-base-substitution signature 29. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS29.tt>}
#' \item{SBS30}{Single-base-substitution signature 30. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS30.tt>}
#' \item{SBS3}{Single-base-substitution signature 3. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS3.tt>}
#' \item{SBS31}{Single-base-substitution signature 31. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS31.tt>}
#' \item{SBS32}{Single-base-substitution signature 32. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS32.tt>}
#' \item{SBS33}{Single-base-substitution signature 33. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS33.tt>}
#' \item{SBS34}{Single-base-substitution signature 34. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS34.tt>}
#' \item{SBS35}{Single-base-substitution signature 35. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS35.tt>}
#' \item{SBS36}{Single-base-substitution signature 36. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS36.tt>}
#' \item{SBS37}{Single-base-substitution signature 37. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS37.tt>}
#' \item{SBS38}{Single-base-substitution signature 38. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS38.tt>}
#' \item{SBS39}{Single-base-substitution signature 39. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS39.tt>}
#' \item{SBS40}{Single-base-substitution signature 40. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS40.tt>}
#' \item{SBS4}{Single-base-substitution signature 4. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS4.tt>}
#' \item{SBS41}{Single-base-substitution signature 41. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS41.tt>}
#' \item{SBS42}{Single-base-substitution signature 42. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS42.tt>}
#' \item{SBS43}{Single-base-substitution signature 43. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS43.tt>}
#' \item{SBS44}{Single-base-substitution signature 44. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS44.tt>}
#' \item{SBS45}{Single-base-substitution signature 45. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS45.tt>}
#' \item{SBS46}{Single-base-substitution signature 46. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS46.tt>}
#' \item{SBS47}{Single-base-substitution signature 47. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS47.tt>}
#' \item{SBS48}{Single-base-substitution signature 48. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS48.tt>}
#' \item{SBS49}{Single-base-substitution signature 49. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS49.tt>}
#' \item{SBS5}{Single-base-substitution signature 5. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS5.tt>}
#' \item{SBS50}{Single-base-substitution signature 50. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS50.tt>}
#' \item{SBS51}{Single-base-substitution signature 51. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS51.tt>}
#' \item{SBS52}{Single-base-substitution signature 52. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS52.tt>}
#' \item{SBS53}{Single-base-substitution signature 53. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS53.tt>}
#' \item{SBS54}{Single-base-substitution signature 54. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS54.tt>}
#' \item{SBS55}{Single-base-substitution signature 55. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS55.tt>}
#' \item{SBS56}{Single-base-substitution signature 56. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS56.tt>}
#' \item{SBS57}{Single-base-substitution signature 57. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS57.tt>}
#' \item{SBS58}{Single-base-substitution signature 58. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS58.tt>}
#' \item{SBS59}{Single-base-substitution signature 59. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS59.tt>}
#' \item{SBS6}{Single-base-substitution signature 6. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS6.tt>}
#' \item{SBS60}{Single-base-substitution signature 60. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS60.tt>}
#' \item{SBS7a}{Single-base-substitution signature 7a. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7a.tt>}
#' \item{SBS7b}{Single-base-substitution signature 7b. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7b.tt>}
#' \item{SBS7c}{Single-base-substitution signature 7c. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7c.tt>}
#' \item{SBS7d}{Single-base-substitution signature 7d. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7d.tt>}
#' \item{SBS8}{Single-base-substitution signature 8. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS8.tt>}
#' \item{SBS9}{Single-base-substitution signature 9. See <https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS9.tt>}
#' }
#'
#' @docType data
......
#' @title Graphical display of a table with circles of varying scales and colours.
#'
#' The code is inspired by the [gridExtra::tableGrob()] function.
#' The code is inspired by the \code{tableGrob} function \code{gridExtra}
#'
#' @description Create a gtable containing circle grobs representing a numeric matrix.
#' @param dscale a matrix
......
......@@ -11,7 +11,70 @@ A data frame with 2780 rows and 68 variables
\item{Sample.Names}{Unique tumour identifiers}
\item{Accuracy}{Cosine similarity between the tumour's mutational profile and the reconstructed mutational profile}
\item{SBS1}{Single-base-substitution signature 1. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS1.tt}}
...
\item{SBS10a}{Single-base-substitution signature 10a. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS10a.tt}}
\item{SBS10b}{Single-base-substitution signature 10b. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS10b.tt}}
\item{SBS11}{Single-base-substitution signature 11. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS11.tt}}
\item{SBS12}{Single-base-substitution signature 12. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS12.tt}}
\item{SBS13}{Single-base-substitution signature 13. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS13.tt}}
\item{SBS14}{Single-base-substitution signature 14. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS14.tt}}
\item{SBS15}{Single-base-substitution signature 15. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS15.tt}}
\item{SBS16}{Single-base-substitution signature 16. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS16.tt}}
\item{SBS17a}{Single-base-substitution signature 17a. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS17a.tt}}
\item{SBS17b}{Single-base-substitution signature 17b. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS17b.tt}}
\item{SBS18}{Single-base-substitution signature 18. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS18.tt}}
\item{SBS19}{Single-base-substitution signature 19. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS19.tt}}
\item{SBS20}{Single-base-substitution signature 20. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS20.tt}}
\item{SBS2}{Single-base-substitution signature 2. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS2.tt}}
\item{SBS21}{Single-base-substitution signature 21. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS21.tt}}
\item{SBS22}{Single-base-substitution signature 22. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS22.tt}}
\item{SBS23}{Single-base-substitution signature 23. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS23.tt}}
\item{SBS24}{Single-base-substitution signature 24. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS24.tt}}
\item{SBS25}{Single-base-substitution signature 25. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS25.tt}}
\item{SBS26}{Single-base-substitution signature 26. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS26.tt}}
\item{SBS27}{Single-base-substitution signature 27. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS27.tt}}
\item{SBS28}{Single-base-substitution signature 28. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS28.tt}}
\item{SBS29}{Single-base-substitution signature 29. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS29.tt}}
\item{SBS30}{Single-base-substitution signature 30. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS30.tt}}
\item{SBS3}{Single-base-substitution signature 3. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS3.tt}}
\item{SBS31}{Single-base-substitution signature 31. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS31.tt}}
\item{SBS32}{Single-base-substitution signature 32. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS32.tt}}
\item{SBS33}{Single-base-substitution signature 33. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS33.tt}}
\item{SBS34}{Single-base-substitution signature 34. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS34.tt}}
\item{SBS35}{Single-base-substitution signature 35. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS35.tt}}
\item{SBS36}{Single-base-substitution signature 36. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS36.tt}}
\item{SBS37}{Single-base-substitution signature 37. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS37.tt}}
\item{SBS38}{Single-base-substitution signature 38. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS38.tt}}
\item{SBS39}{Single-base-substitution signature 39. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS39.tt}}
\item{SBS40}{Single-base-substitution signature 40. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS40.tt}}
\item{SBS4}{Single-base-substitution signature 4. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS4.tt}}
\item{SBS41}{Single-base-substitution signature 41. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS41.tt}}
\item{SBS42}{Single-base-substitution signature 42. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS42.tt}}
\item{SBS43}{Single-base-substitution signature 43. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS43.tt}}
\item{SBS44}{Single-base-substitution signature 44. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS44.tt}}
\item{SBS45}{Single-base-substitution signature 45. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS45.tt}}
\item{SBS46}{Single-base-substitution signature 46. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS46.tt}}
\item{SBS47}{Single-base-substitution signature 47. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS47.tt}}
\item{SBS48}{Single-base-substitution signature 48. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS48.tt}}
\item{SBS49}{Single-base-substitution signature 49. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS49.tt}}
\item{SBS5}{Single-base-substitution signature 5. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS5.tt}}
\item{SBS50}{Single-base-substitution signature 50. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS50.tt}}
\item{SBS51}{Single-base-substitution signature 51. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS51.tt}}
\item{SBS52}{Single-base-substitution signature 52. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS52.tt}}
\item{SBS53}{Single-base-substitution signature 53. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS53.tt}}
\item{SBS54}{Single-base-substitution signature 54. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS54.tt}}
\item{SBS55}{Single-base-substitution signature 55. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS55.tt}}
\item{SBS56}{Single-base-substitution signature 56. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS56.tt}}
\item{SBS57}{Single-base-substitution signature 57. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS57.tt}}
\item{SBS58}{Single-base-substitution signature 58. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS58.tt}}
\item{SBS59}{Single-base-substitution signature 59. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS59.tt}}
\item{SBS6}{Single-base-substitution signature 6. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS6.tt}}
\item{SBS60}{Single-base-substitution signature 60. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS60.tt}}
\item{SBS7a}{Single-base-substitution signature 7a. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7a.tt}}
\item{SBS7b}{Single-base-substitution signature 7b. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7b.tt}}
\item{SBS7c}{Single-base-substitution signature 7c. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7c.tt}}
\item{SBS7d}{Single-base-substitution signature 7d. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS7d.tt}}
\item{SBS8}{Single-base-substitution signature 8. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS8.tt}}
\item{SBS9}{Single-base-substitution signature 9. See \url{https://cancer.sanger.ac.uk/cosmic/signatures/SBS/SBS9.tt}}
}
}
\source{
......
......@@ -4,7 +4,7 @@
\alias{table_extra_grob}
\title{Graphical display of a table with circles of varying scales and colours.
The code is inspired by the \code{\link[gridExtra:tableGrob]{gridExtra::tableGrob()}} function.}
The code is inspired by the \code{tableGrob} function \code{gridExtra}}
\usage{
table_extra_grob(
dscale,
......
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