v0.99.9 reorganize test data+add some tests

.Rbuildignore

 ^renv$
 ^renv\.lock$
 ^LICENSE\.md$
+^\.tool-versions$
+^\.gitlab-ci\.yml$
+^.*\.pdf$
+^.*\.tar\.gz$
+Makefile
+data-raw
+assets
+tags

DESCRIPTION

 Package: tableExtra
-Title: Draws an awesome table
-Version: 0.99.4
+Title: Draws An Awesome Table
+Version: 0.99.9
 Authors@R: 
     person(given = "Yoann",
            family = "Pradat",
@@ -15,6 +15,7 @@ RoxygenNote: 7.1.1
 Suggests: 
     testthat,
     dplyr,
+    forcats,
     tibble 
 Depends: 
     R (>= 3.5.0)

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(gtable_cbind)
+export(gtable_legend)
 export(gtable_rbind)
 export(table_extra_grob)
 export(ttheme_awesome)

R/gtables.R

@@ -23,10 +23,10 @@
 #' @author Yoann Pradat
 #' @keywords internal
 gtable_table <- function(d, widths, heights,
-                         fg_fun = text_grob, fg_params = list(),
-                         bg_fun = NULL, bg_params = NULL,
-                         padding = unit(c(4, 4), "mm"),
-                         name = "table", vp = NULL, rep_mode="row", ...){
+                         fg_fun=text_grob, fg_params=list(),
+                         bg_fun=NULL, bg_params=NULL,
+                         padding=unit(c(4, 4), "mm"),
+                         name="table", vp=NULL, rep_mode="row", ...){
 
   d <- as.matrix(d)
 
@@ -85,7 +85,9 @@ gtable_table <- function(d, widths, heights,
 #' @param title_x \code{unit} specifying the x position of the title
 #' @param title_y \code{unit} specifying the x position of the title
 #' @param title_label character vector
-#' @param padding \code{unit.list} object specifying the padding between adjacent cells.
+#' @param padding numeric vector specifying the padding between adjacent cells.
+#' @param size_unit character vector defining the unit used for sizes. See \code{grid::unit} for all possible
+#' specifications.
 #' @param name optional name of the grob
 #' @param vp optional viewport
 #' @param ... additional parameters passed to \code{add_table_params}.
@@ -94,11 +96,14 @@ gtable_table <- function(d, widths, heights,
 #' @import gtable
 #'
 #' @author Yoann Pradat
-#' @keywords internal
+#' @export
 gtable_legend <- function(d, labels, widths, heights, fg_fun, fg_params, bg_fun=NULL, bg_params=NULL,
                           title_x=NULL, title_y=NULL, title_label="Title", title_gp=gpar(fontsize=10), 
-                          labels_pad=unit(-1,"mm"), labels_gp=gpar(fontsize=6), padding=unit(0.3, "mm"),
-                          name="legend", vp=NULL, orientation="horizontal", ...){
+                          labels_pad=-1, labels_gp=gpar(fontsize=6), padding=0.3,
+                          size_unit="mm", name="legend", vp=NULL, orientation="horizontal", ...){
+
+  labels_pad <- unit(labels_pad, size_unit)
+  padding <- unit(padding, size_unit)
 
   # legend body
   g <- gtable_table(d, name=name,
@@ -108,7 +113,7 @@ gtable_legend <- function(d, labels, widths, heights, fg_fun, fg_params, bg_fun=
                     bg_fun=bg_fun, 
                     fg_params=fg_params, 
                     bg_params=bg_params, 
-                    padding=padding, ...)
+                    padding=padding, vp=vp, ...)
 
   # legend title
   g_title <- textGrob(label=title_label, 
@@ -120,7 +125,7 @@ gtable_legend <- function(d, labels, widths, heights, fg_fun, fg_params, bg_fun=
 
   # legend labels
   if (orientation=="horizontal"){
-    x <- unit(0, attr(padding, "unit"))
+    x <- unit(0, size_unit)
     for (i in 1:length(labels)){
       g_label <- textGrob(label=labels[i], 
                           x=x,

R/pcwag_counts-data.R

-#' Mutation counts attributed to each mutational signature in each tumour.
-#'
-#' Data from the mutational signature analysis of Alexandrov et al. on the PCAWG data.
-#' The data is available as supplementary data to the paper "The repertoire of mutational signatures in human cancer"
-#' on the Synapse data repository syn11738669
-#' 
-#' \code{pcawg_counts} contains the mutation counts as attributed by the SigProfiler algorithm on the
-#' Single-Base-Substitution (SBSs) mutation catalogs of 2780 WGS tumours from the PCAWG.
-#'
-#' @format A data frame with 2780 rows and 68 variables
-#' \describe{
-#'   \item{Cancer.Types}{37 different cancer types}
-#'   \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
-#' @usage data(pcawg_counts)
-#' @keywords datasets
-#'
-#' @references 
-#' Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. 
-#' Nature 578, 94–101 (2020). \url{https://doi.org/10.1038/s41586-020-1943-3}
-#'
-#' @source Synapse collaborative compute space, <https://www.synapse.org/#!Synapse:syn11804065>
-#'
-#' @examples
-#' data(pcawg_counts)
-"pcawg_counts"

R/table_extra_grob.R

@@ -39,7 +39,7 @@ table_extra_grob <- function(dscale, dcolor=NULL,
   widths <- rep(theme$core$size, ncol(dscale))
   heights <- rep(theme$core$size, nrow(dscale))
 
-  g <- gtable_table(dscale, name="circle",
+  g <- gtable_table(dscale, name="core",
                     widths=widths,
                     heights=heights,
                     fg_fun=theme$core$fg_fun, 

R/table_params.R

@@ -155,7 +155,7 @@ add_table_params <- function(d, params, fun, ...){
   } else if (all.equal(fun, rect_grob)==T) { 
     extra_params <- table_params_rect(d, ...)
   } else {
-    stop("unsupported value of fun")
+    stop("Unsupported value of fun")
   }
 
   return(c(params, extra_params))

R/ttheme_awesome.R

@@ -10,7 +10,9 @@
 #' @param color_breaks bin breaks for color palette for core foreground grobs
 #' @param rep_mode 'col' or 'row'. Used when recycling fg_params or bg_params to make a matrix of params.
 #' @param parse logical, default behaviour for parsing text as plotmath
-#' @param padding length-2 unit vector specifying the horizontal and vertical padding of text within each cell
+#' @param size_unit character vector defining the unit used for sizes. See \code{grid::unit} for all possible
+#' specifications.
+#' @param padding length-2 vector specifying the horizontal and vertical padding of text within each cell
 #' @param ... extra parameters added to the theme list
 #'
 #' @importFrom utils modifyList
@@ -21,35 +23,34 @@
 ttheme_awesome <- function(base_size=8, 
                            base_colour="black", 
                            base_family="",
-                           core_size=unit(10, "mm"),
+                           core_size=10,
                            scale_breaks=10,
                            scale_ratio=0.25,
                            color_palette="black",
                            color_breaks=NULL,
                            rep_mode="col",
                            parse=FALSE, 
-                           padding=unit(c(0.3,0.3), "mm"), ...){
+                           size_unit="mm",
+                           padding=c(0.3,0.3), ...){
 
   # The code `do.call(mapply, c(fg_params, list(FUN = fg_fun, SIMPLIFY=FALSE)))`
   # cannot accomodate variables of the class `unit`.  
   # Current fix: split the value and the unit.
-  core_size_value <- as.numeric(core_size)
-  core_size_unit <- attr(core_size, "unit")
   core <- list(fg_fun=circle_grob, 
                fg_params=list(col="white", lwd=0),
                bg_fun=rect_grob, 
                bg_params=list(fill=c("#f2f2f2","#e5e5e5"),
-                              width=core_size_value, 
-                              height=core_size_value,
-                              default.units=core_size_unit,
+                              width=core_size, 
+                              height=core_size,
+                              default.units=size_unit,
                               lwd=0, col="white"),
                rep_mode=rep_mode,
-               size=core_size,
+               size=unit(core_size,size_unit),
                scale_breaks=scale_breaks,
                scale_ratio=scale_ratio,
                color_palette=color_palette,
                color_breaks=color_breaks,
-               padding=padding)
+               padding=unit(padding, size_unit))
 
   colhead <- list(fg_fun=text_grob, 
                   fg_params=list(parse=parse, col=base_colour,
@@ -61,10 +62,10 @@ ttheme_awesome <- function(base_size=8,
                                  rot=90),
                   bg_fun=rect_grob, 
                   bg_params=list(fill=c("white"),
-                                 width=core_size_value,
-                                 default.units=core_size_unit,
+                                 width=core_size,
+                                 default.units=size_unit,
                                  lwd=0, col="white"),
-                  padding=padding)
+                  padding=unit(padding, size_unit))
 
   colmore <- list(fg_fun=text_grob, 
                   fg_params=list(parse=parse, col=base_colour,
@@ -76,10 +77,10 @@ ttheme_awesome <- function(base_size=8,
                                  rot=90),
                   bg_fun=rect_grob, 
                   bg_params=list(fill=c("white"),
-                                 width=core_size_value,
-                                 default.units=core_size_unit,
+                                 width=core_size,
+                                 default.units=size_unit,
                                  lwd=0, col="white"),
-                  padding=padding)
+                  padding=unit(padding, size_unit))
 
   rowhead <- list(fg_fun=text_grob, 
                   fg_params=list(parse=parse, col=base_colour,
@@ -90,10 +91,10 @@ ttheme_awesome <- function(base_size=8,
                                  x=0.95),
                   bg_fun=rect_grob, 
                   bg_params=list(fill=c("white"),
-                                 height=core_size_value,
-                                 default.units=core_size_unit,
+                                 height=core_size,
+                                 default.units=size_unit,
                                  lwd=0, col="white"),
-                  padding=padding)
+                  padding=unit(padding, size_unit))
 
   rowmore <- list(fg_fun=text_grob, 
                   fg_params=list(parse=parse, col=base_colour,
@@ -104,10 +105,10 @@ ttheme_awesome <- function(base_size=8,
                                  x=0),
                   bg_fun=rect_grob, 
                   bg_params=list(fill=c("white"),
-                                 height=core_size_value,
-                                 default.units=core_size_unit,
+                                 height=core_size,
+                                 default.units=size_unit,
                                  lwd=0, col="white"),
-                  padding=padding)
+                  padding=unit(padding, size_unit))
 
   default <- list(core=core,
                   colhead=colhead,

data-raw/cosmic_v3_aetiologies.csv

-"Aetiology","Signature"
-"Spontaneous deamination of 5-methylcytosine (clock-like signature)","SBS1"
-"Activity of APOBEC family of cytidine deaminases","SBS2"
-"Defective homologous recombination DNA damage repair","SBS3"
-"Tobacco smoking","SBS4"
-"Unknown (clock-like signature)","SBS5"
-"Defective DNA mismatch repair","SBS6"
-"Ultraviolet light exposure","SBS7a"
-"Ultraviolet light exposure","SBS7b"
-"Ultraviolet light exposure","SBS7c"
-"Ultraviolet light exposure","SBS7d"
-"Unknown","SBS8"
-"Polimerase eta somatic hypermutation activity","SBS9"
-"Polymerase epsilon exonuclease domain mutations","SBS10a"
-"Polymerase epsilon exonuclease domain mutations","SBS10b"
-"Temozolomide treatment","SBS11"
-"Unknown","SBS12"
-"Activity of APOBEC family of cytidine deaminases","SBS13"
-"Concurrent polymerase epsilon mutation and defective DNA mismatch repair","SBS14"
-"Defective DNA mismatch repair","SBS15"
-"Unknown","SBS16"
-"Unknown","SBS17a"
-"Unknown","SBS17b"
-"Damage by reactive oxygen species","SBS18"
-"Unknown","SBS19"
-"Concurrent POLD1 mutations and defective DNA mismatch repair","SBS20"
-"Defective DNA mismatch repair","SBS21"
-"Aristolochic acid exposure","SBS22"
-"Unknown","SBS23"
-"Aflatoxin exposure","SBS24"
-"Chemotherapy treatment","SBS25"
-"Defective DNA mismatch repair","SBS26"
-"Possible sequencing artefact","SBS27"
-"Unknown","SBS28"
-"Tobacco chewing","SBS29"
-"Defective DNA base excision repair due to NTHL1 mutations","SBS30"
-"Platinum chemotherapy treatment","SBS31"
-"Azathioprine treatment","SBS32"
-"Unknown","SBS33"
-"Unknown","SBS34"
-"Platinum chemotherapy treatment","SBS35"
-"Defective DNA base excision repair due to MUTYH mutations","SBS36"
-"Unknown","SBS37"
-"Indirect effect of ultraviolet light","SBS38"
-"Unknown","SBS39"
-"Unknown","SBS40"
-"Unknown","SBS41"
-"Haloalkane exposure","SBS42"
-"Possible sequencing artefact","SBS43"
-"Defective DNA mismatch repair","SBS44"
-"Possible sequencing artefact","SBS45"
-"Possible sequencing artefact","SBS46"
-"Possible sequencing artefact","SBS47"
-"Possible sequencing artefact","SBS48"
-"Possible sequencing artefact","SBS49"
-"Possible sequencing artefact","SBS50"
-"Possible sequencing artefact","SBS51"
-"Possible sequencing artefact","SBS52"
-"Possible sequencing artefact","SBS53"
-"Possible sequencing artefact","SBS54"
-"Possible sequencing artefact","SBS55"
-"Possible sequencing artefact","SBS56"
-"Possible sequencing artefact","SBS57"
-"Possible sequencing artefact","SBS58"
-"Possible sequencing artefact","SBS59"
-"Possible sequencing artefact","SBS60"
-"Activity of activation-induced cytidine deaminase (AID)","SBS84"
-"Indirect effects of activation-induced cytidine deaminase (AID)","SBS85"
-"Unknown chemotherapy treatment","SBS86"
-"Thiopurine chemotherapy treatment","SBS87"
-"Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)","SBS88"
-"Unknown","SBS89"
-"Duocarmycin exposure","SBS90"

man/gtable_legend.Rd

@@ -17,9 +17,10 @@ gtable_legend(
   title_y = NULL,
   title_label = "Title",
   title_gp = gpar(fontsize = 10),
-  labels_pad = unit(-1, "mm"),
+  labels_pad = -1,
   labels_gp = gpar(fontsize = 6),
-  padding = unit(0.3, "mm"),
+  padding = 0.3,
+  size_unit = "mm",
   name = "legend",
   vp = NULL,
   orientation = "horizontal",
@@ -47,7 +48,10 @@ gtable_legend(
 
 \item{title_label}{character vector}
 
-\item{padding}{\code{unit.list} object specifying the padding between adjacent cells.}
+\item{padding}{numeric vector specifying the padding between adjacent cells.}
+
+\item{size_unit}{character vector defining the unit used for sizes. See \code{grid::unit} for all possible
+specifications.}
 
 \item{name}{optional name of the grob}
 
@@ -64,4 +68,3 @@ Build a grob with a legend inside.
 \author{
 Yoann Pradat
 }
-\keyword{internal}

man/pcawg_counts.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pcwag_counts-data.R
-\docType{data}
-\name{pcawg_counts}
-\alias{pcawg_counts}
-\title{Mutation counts attributed to each mutational signature in each tumour.}
-\format{
-A data frame with 2780 rows and 68 variables
-\describe{
-\item{Cancer.Types}{37 different cancer types}
-\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{
-Synapse collaborative compute space, \url{https://www.synapse.org/#!Synapse:syn11804065}
-}
-\usage{
-data(pcawg_counts)
-}
-\description{
-Data from the mutational signature analysis of Alexandrov et al. on the PCAWG data.
-The data is available as supplementary data to the paper "The repertoire of mutational signatures in human cancer"
-on the Synapse data repository syn11738669
-}
-\details{
-\code{pcawg_counts} contains the mutation counts as attributed by the SigProfiler algorithm on the
-Single-Base-Substitution (SBSs) mutation catalogs of 2780 WGS tumours from the PCAWG.
-}
-\examples{
-data(pcawg_counts)
-}
-\references{
-Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer.
-Nature 578, 94–101 (2020). \url{https://doi.org/10.1038/s41586-020-1943-3}
-}
-\keyword{datasets}

man/ttheme_awesome.Rd

@@ -8,14 +8,15 @@ ttheme_awesome(
   base_size = 8,
   base_colour = "black",
   base_family = "",
-  core_size = unit(10, "mm"),
+  core_size = 10,
   scale_breaks = 10,
   scale_ratio = 0.25,
   color_palette = "black",
   color_breaks = NULL,
   rep_mode = "col",
   parse = FALSE,
-  padding = unit(c(0.3, 0.3), "mm"),
+  size_unit = "mm",
+  padding = c(0.3, 0.3),
   ...
 )
 }
@@ -40,7 +41,10 @@ ttheme_awesome(
 
 \item{parse}{logical, default behaviour for parsing text as plotmath}
 
-\item{padding}{length-2 unit vector specifying the horizontal and vertical padding of text within each cell}
+\item{size_unit}{character vector defining the unit used for sizes. See \code{grid::unit} for all possible
+specifications.}
+
+\item{padding}{length-2 vector specifying the horizontal and vertical padding of text within each cell}
 
 \item{...}{extra parameters added to the theme list}
 }

renv.lock

@@ -74,10 +74,10 @@
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.0.2",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "d0509913b27ea898189ee664b6030dc2"
+      "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68"
     },
     "ellipsis": {
       "Package": "ellipsis",
@@ -130,10 +130,10 @@
     },
     "lifecycle": {
       "Package": "lifecycle",
-      "Version": "0.2.0",
+      "Version": "1.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "361811f31f71f8a617a9a68bf63f1f42"
+      "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -221,10 +221,10 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "0.4.8",
+      "Version": "0.4.10",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "843a6af51414bce7f8a8e372f11d6cd0"
+      "Hash": "599df23c40a4fce9c7b4764f28c37857"
     },
     "rprojroot": {
       "Package": "rprojroot",
@@ -270,10 +270,10 @@
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.3.5",
+      "Version": "0.3.6",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "d25c5bea636cf892edbfd64fc3d20c20"
+      "Hash": "5cf1957f93076c19fdc81d01409d240b"
     },
     "waldo": {
       "Package": "waldo",

tests/testthat/helper.R

@@ -3,9 +3,11 @@ suppressMessages(library(tibble))
 
 load("testdata/DBS.rda")
 load("testdata/DEXP.rda")
+load("testdata/pcawg_counts.rda")
+load("testdata/sbs_aetiologies.rda")
 
 plot_grob <- function(g, name, width=NULL, height=NULL){
-  grDevices::pdf(file=file.path("pdfs_plots", name),
+  grDevices::pdf(file=file.path(system.file("tests", "testthat", "pdfs_plots", package="tableExtra"), name),
                  width=width,
                  height=height,
                  onefile=T)
@@ -13,6 +15,3 @@ plot_grob <- function(g, name, width=NULL, height=NULL){
   grDevices::dev.off()
   invisible(list(plot_success=T))
 }
-
-# Aetiologies for PCAWG
-SBS_aetiology <- read.csv("../../data-raw/cosmic_v3_aetiologies.csv", stringsAsFactors=F)