Commit 4bec439f authored by Pradat Yoann's avatar Pradat Yoann
Browse files

rm tags from remote

parent 128e66ba
!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/
!_TAG_PROGRAM_NAME Exuberant Ctags //
!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/
!_TAG_PROGRAM_VERSION 5.8 //
add_table_params R/table_params.R /^add_table_params <- function(d, params, fun, ...){$/;" f
align_2 R/gtable_utils.R /^align_2 <- function(x, y, along = 1L, join = "outer") {$/;" f
aligned R/gtable_utils.R /^ aligned <- align_2(x, y, along = along, join = join)$/;" v
assays tests/testthat/testdata/DBS.R /^assays <- SimpleList()$/;" g
assays tests/testthat/testdata/DEXP.R /^assays <- SimpleList()$/;" g
bg_fun R/gtables.R /^ bg_fun = rect_grob, bg_params = list(),$/;" v
bg_fun R/test.R /^# bg_fun = rect_grob, $/;" v
bg_fun R/test.R /^# bg_fun = rect_grob, $/;" v
bg_fun tests/testthat/test-gtable_utils.R /^ bg_fun = theme$colhead$bg_fun, $/;" v
bg_fun tests/testthat/test-gtable_utils.R /^ bg_fun = theme$core$bg_fun, $/;" v
bg_fun tests/testthat/test-gtable_utils.R /^ bg_fun = theme$rowhead$bg_fun, $/;" v
bg_fun tests/testthat/test-gtable_utils.R /^ bg_fun = theme$colhead$bg_fun, $/;" v
bg_params R/gtables.R /^ bg_params <- tb_params[["bg_params"]]$/;" v
bg_params R/table_params.R /^ bg_params <- lapply(bg_params, rep_ifshort, n = n, nc = nc, nr = nr)$/;" v
bg_params R/test.R /^# bg_params = list(fill = c("grey80"), $/;" v
bg_params R/test.R /^# bg_params = list(fill=NA, lwd=1.5, col="white"),$/;" v
bg_params R/test.R /^# bg_params = list(fill = c("grey95","grey90"), $/;" v
bg_params tests/testthat/test-gtable_utils.R /^ bg_params = theme$colhead$bg_params, $/;" v
bg_params tests/testthat/test-gtable_utils.R /^ bg_params = theme$core$bg_params, $/;" v
bg_params tests/testthat/test-gtable_utils.R /^ bg_params = theme$rowhead$bg_params, $/;" v
bg_params tests/testthat/test-gtable_utils.R /^ bg_params = theme$colhead$bg_params, $/;" v
bkgds_grobs R/gtables.R /^ bkgds_grobs <- matrix(bkgds, ncol = nc, byrow = FALSE)$/;" v
breaks R/other_utils.R /^ breaks <- (breaks-d_min)\/(d_max-d_min)$/;" v
breaks_scale R/other_utils.R /^breaks_scale <- function(d, d_min=NULL, d_max=NULL, breaks=10){$/;" f
cbind_2 R/gtable_utils.R /^cbind_2 <- function(x, y, size = "max", width=NULL) {$/;" f
circle_grob R/vectorgrobs.R /^circle_grob <- function(r=unit(5, "mm"),$/;" f
col R/test.R /^# col <- matrix(list(a, b, c), ncol = 1)$/;" v
col R/vectorgrobs.R /^ col = "black", $/;" v
col R/vectorgrobs.R /^ col = "black", $/;" v
col R/vectorgrobs.R /^ col = "black",$/;" v
col tests/testthat/test-gtable_utils.R /^ col <- t(colnames(d))$/;" v
colData tests/testthat/testdata/DBS.R /^ colData = colData,$/;" v
colData tests/testthat/testdata/DBS.R /^colData <- data.frame(name=cols, description=cols.desc, stringsAsFactors=F)$/;" g
colData tests/testthat/testdata/DEXP.R /^ colData = colData,$/;" v
colData tests/testthat/testdata/DEXP.R /^colData <- data.frame(name=cols, description=cols.desc, stringsAsFactors=F)$/;" g
col_widths R/other_utils.R /^col_widths <- function(m){$/;" f
colhead R/test.R /^# colhead = colhead,$/;" v
colhead R/test.R /^# colhead <- list(fg_fun = text_grob, $/;" v
colhead R/theme_awesome.R /^ colhead <- list(fg_fun=text_grob, $/;" v
colmore R/theme_awesome.R /^ colmore <- list(fg_fun=text_grob, $/;" v
colnames R/gtable_utils.R /^ colnames = missing)$/;" v
color_breaks tests/testthat/test-table_extra_grob.R /^ color_breaks <- c(-2, 0, 2)$/;" v
color_breaks tests/testthat/test-table_extra_grob.R /^ color_breaks <- c(0, 0.001,0.005,0.008,0.01,0.02,0.03,0.05,0.1,0.5,1)$/;" v
color_breaks tests/testthat/test-table_extra_grob.R /^ color_breaks <- c(0, 0.05, 0.1, 0.25, 0.5, 1, 2.5, 5, 10, 25, 1e6)$/;" v
color_palette tests/testthat/test-table_extra_grob.R /^ color_palette <- c("#6e0d25", "#c6ca53")$/;" v
color_palette tests/testthat/test-table_extra_grob.R /^ color_palette <- c("#ffc651", "#ffa759", "#ff8962", "#ff6b6b", "#cc6999", "#9968c8", "#6767f8", "#4459ce", "#224ba5", $/;" v
cols R/test.R /^# cols = colnames(DBS)$/;" v
cols tests/testthat/testdata/DBS.R /^cols <- c("Biliary-AdenoCA", "Bladder-TCC", "Bone-Osteosarc", "Bone-Other", "Breast", "Cervix", "CNS-GBM", $/;" g
cols tests/testthat/testdata/DEXP.R /^cols <- c("Biliary-AdenoCA", "Bladder-TCC", "Bone-Osteosarc", "Bone-Other", "Breast", "Cervix", "CNS-GBM", $/;" g
cols.desc tests/testthat/testdata/DBS.R /^cols.desc <- c(8, 10, 0, 0, 18, 0, 2, 0, 0, 0, 13, 1)$/;" g
cols.desc tests/testthat/testdata/DEXP.R /^cols.desc <- c(8, 10, 0, 0, 18, 0, 2, 0, 0, 0, 13, 1)$/;" g
cols_more tests/testthat/test-table_extra_grob.R /^ cols_more <- list("n="=SummarizedExperiment::colData(DBS)$description)$/;" v
cols_more tests/testthat/test-table_extra_grob.R /^ cols_more <- list("n="=dscale$n)$/;" v
combine R/gtable_utils.R /^combine <- function (..., along = 1L, join = "outer") {$/;" f
combine_2 R/gtable_utils.R /^combine_2 <- function(x, y, along = 1L, join = "outer") {$/;" f
core R/test.R /^# core <- list(fg_fun = text_grob, $/;" v
core R/theme_awesome.R /^ core <- list(fg_fun=circle_grob, $/;" v
core_size_value R/theme_awesome.R /^ core_size_value <- as.numeric(core_size)$/;" v
d R/gtables.R /^ d <- as.matrix(d)$/;" v
d R/table_params.R /^ d <- as.matrix(color_palette, nrow=nrow(d), ncol=ncol(d))$/;" v
d R/table_params.R /^ d <- as.vector(d)$/;" v
d R/table_params.R /^ d <- breaks_scale(d=d, d_min=d_min, d_max=d_max, breaks=scale_breaks)$/;" v
d R/test.R /^# d = assays(DBS)$proportion,$/;" v
d tests/testthat/test-gtable_utils.R /^ d <- matrix(rep(d, 5), nrow=5, byrow=T)$/;" v
d tests/testthat/test-gtable_utils.R /^ d <- t(SummarizedExperiment::colData(DBS)$description)$/;" v
d tests/testthat/test-gtables.R /^ d <- matrix(rep(d, 5), nrow=5, byrow=T)$/;" v
d tests/testthat/test-gtables.R /^ d <- t(SummarizedExperiment::colData(DBS)$description)$/;" v
data tests/testthat/testdata/DBS.R /^data <- matrix(c(rep(0., 12),$/;" g
data tests/testthat/testdata/DEXP.R /^data <- matrix(runif(length(rows)*length(cols), min=0, max=1), nrow=length(rows))$/;" g
data tests/testthat/testdata/DEXP.R /^data <- matrix(sample(c(-1,1), size=length(rows)*length(cols), replace=T), nrow=length(rows))$/;" g
dcolor tests/testthat/test-table_extra_grob.R /^ dcolor <- column_to_rownames(.data=dcolor, var="Cancer.Types")$/;" v
dcolor tests/testthat/test-table_extra_grob.R /^ dcolor <- pcawg_counts %>%$/;" v
dcolor tests/testthat/test-table_extra_grob.R /^ dcolor <- t(as.matrix(dcolor))$/;" v
dcut R/other_utils.R /^ dcut <- dcut\/max(dcut)$/;" v
dcut R/other_utils.R /^ dcut <- matrix(dint, nrow=nrow(d), byrow=F)$/;" v
default.units R/vectorgrobs.R /^ default.units = default.units,$/;" v
default.units R/vectorgrobs.R /^ default.units = default.units,$/;" v
dint R/other_utils.R /^ dint <- (breaks[dint] + breaks[dint+1])\/2$/;" v
dscale tests/testthat/test-table_extra_grob.R /^ dscale <- -log10(SummarizedExperiment::assays(DEXP)$pvalue) + 1$/;" v
dscale tests/testthat/test-table_extra_grob.R /^ dscale <- column_to_rownames(.data=dscale, var="Cancer.Types")$/;" v
dscale tests/testthat/test-table_extra_grob.R /^ dscale <- pcawg_counts %>%$/;" v
dscale tests/testthat/test-table_extra_grob.R /^ dscale <- t(as.matrix(dscale))$/;" v
each R/gtables.R /^ l=rep(seq_len(nc), each = nr), z=0, $/;" v
error R/vectorgrobs.R /^ error = function(e) label)$/;" f
extra_params R/table_params.R /^ extra_params <- table_params_circle(d, ...)$/;" v
extra_params R/table_params.R /^ extra_params <- table_params_text(d)$/;" v
fg_fun R/gtables.R /^ fg_fun = text_grob, fg_params = list(),$/;" v
fg_fun tests/testthat/test-gtable_utils.R /^ fg_fun = theme$colhead$fg_fun, $/;" v
fg_fun tests/testthat/test-gtable_utils.R /^ fg_fun = theme$core$fg_fun, $/;" v
fg_fun tests/testthat/test-gtable_utils.R /^ fg_fun = theme$rowhead$fg_fun, $/;" v
fg_fun tests/testthat/test-gtable_utils.R /^ fg_fun = theme$colhead$fg_fun, $/;" v
fg_params R/gtables.R /^ fg_params <- tb_params[["fg_params"]]$/;" v
fg_params R/table_params.R /^ fg_params <- lapply(fg_params, rep_ifshort, n = n, nc = nc, nr = nr)$/;" v
fg_params R/test.R /^# fg_params = list(parse=parse, col=base_colour,$/;" v
fg_params R/test.R /^# fg_params = list(parse=parse, col=base_colour,$/;" v
fg_params tests/testthat/test-gtable_utils.R /^ fg_params = theme$colhead$fg_params, $/;" v
fg_params tests/testthat/test-gtable_utils.R /^ fg_params = theme$core$fg_params, $/;" v
fg_params tests/testthat/test-gtable_utils.R /^ fg_params = theme$rowhead$fg_params, $/;" v
fg_params tests/testthat/test-gtable_utils.R /^ fg_params = theme$colhead$fg_params, $/;" v
fill R/vectorgrobs.R /^ fill = "black", $/;" v
first R/gtable_utils.R /^ first = x$heights,$/;" v
first R/gtable_utils.R /^ first = x$widths,$/;" v
fixed R/gtable_utils.R /^ fixed = FALSE, trim=TRUE){$/;" v
fontfamily R/test.R /^# fontfamily = base_family),$/;" v
fontfamily R/test.R /^# fontfamily = base_family,$/;" v
fontfamily R/test.R /^# fontfamily = base_family),$/;" v
fontsize R/test.R /^# fontsize = base_size,$/;" v
fontsize R/test.R /^# fontsize = base_size,$/;" v
frgds_grobs R/gtables.R /^ frgds_grobs <- matrix(frgds, ncol = nc, byrow = FALSE)$/;" v
g R/gtables.R /^ g <- gtable_add_col_space(g, padding[1])$/;" v
g R/gtables.R /^ g <- gtable_add_grob(g, bkgds_grobs, $/;" v
g R/gtables.R /^ g <- gtable_add_row_space(g, padding[2])$/;" v
g R/gtables.R /^ g <- gtable_matrix(paste0(name, "-fg"), $/;" v
g R/table_extra_grob.R /^ g <- cbind_2(g, gr, "max", width=theme$rowmore$padding[2])$/;" v
g R/table_extra_grob.R /^ g <- rbind_2(gc, g, "max", height=theme$colmore$padding[1])$/;" v
g R/table_extra_grob.R /^ g <- cbind_2(gr, g, "max", width=theme$rowhead$padding[2])$/;" v
g R/table_extra_grob.R /^ g <- rbind_2(gc, g, "max", height=theme$colhead$padding[1])$/;" v
g R/table_extra_grob.R /^ g <- gtable_table(dscale, name="circle",$/;" v
g tests/testthat/test-gtable_utils.R /^ g <- cbind_2(g1, g2, "max", width=theme$core$padding[2])$/;" v
g tests/testthat/test-gtable_utils.R /^ g <- rbind_2(g1, g2, "max", height=theme$core$padding[1])$/;" v
g tests/testthat/test-gtable_utils.R /^ g <- rbind_2(g1, g2, size="first", height=theme$rowhead$padding[1])$/;" v
g tests/testthat/test-gtable_utils.R /^ g <- rbind_2(g1, g2, size="last", height=theme$core$padding[1])$/;" v
g tests/testthat/test-gtables.R /^ g <- gtable_table(d, name="circle",$/;" v
g tests/testthat/test-table_extra_grob.R /^ g <- table_extra_grob(d, rows=rownames(d), cols=colnames(d),$/;" v
g tests/testthat/test-table_extra_grob.R /^ g <- table_extra_grob(dscale=dscale, dcolor=dcolor, $/;" v
g tests/testthat/test-vectorgrobs.R /^ g <- grid::gTree(children=grid::gList(gr, gc))$/;" v
g tests/testthat/test-vectorgrobs.R /^ g <- rect_grob(width=unit(10, "mm"),$/;" v
g tests/testthat/test-vectorgrobs.R /^ g <- rect_grob(x=unit(0.5, "mm"),$/;" v
g tests/testthat/test-vectorgrobs.R /^ g <- text_grob(label="test",$/;" v
g1 tests/testthat/test-gtable_utils.R /^ g1 <- gtable_table(col, name="colhead-1",$/;" v
g1 tests/testthat/test-gtable_utils.R /^ g1 <- gtable_table(d, name="circle",$/;" v
g1 tests/testthat/test-gtable_utils.R /^ g1 <- gtable_table(d, name="colhead-1",$/;" v
g1 tests/testthat/test-gtable_utils.R /^ g1 <- gtable_table(d, name="rowhead-1",$/;" v
g2 tests/testthat/test-gtable_utils.R /^ g2 <- gtable_table(d, name="circle",$/;" v
g2 tests/testthat/test-gtable_utils.R /^ g2 <- gtable_table(d, name="colhead-2",$/;" v
g2 tests/testthat/test-gtable_utils.R /^ g2 <- gtable_table(d, name="rowhead-2",$/;" v
gc R/table_extra_grob.R /^ gc <- gtable_table(t(cols_m), name="colmore",$/;" v
gc R/table_extra_grob.R /^ gc <- gtable_table(t(cols), name="colhead",$/;" v
gc tests/testthat/test-gtables.R /^ gc <- gtable_table(d, name="colhead",$/;" v
gr R/table_extra_grob.R /^ gr <- gtable_table(rows_m, name="rowmore",$/;" v
gr R/table_extra_grob.R /^ gr <- gtable_table(rows, name="rowhead",$/;" v
gr tests/testthat/test-gtables.R /^ gr <- gtable_table(d, name="rowhead",$/;" v
gr tests/testthat/test-vectorgrobs.R /^ gr <- rect_grob(width=unit(10,"mm"),$/;" v
gtable_cbind R/gtable_utils.R /^gtable_cbind <- function(..., size = "max", z = NULL) {$/;" f
gtable_combine R/gtable_utils.R /^gtable_combine <- function (..., along = 1L, join = "outer") $/;" f
gtable_rbind R/gtable_utils.R /^gtable_rbind <- function(..., size = "max", z = NULL) {$/;" f
gtable_reindex R/gtable_utils.R /^gtable_reindex <- function(x, index, along = 1L) {$/;" f
gtable_remove_grob R/gtable_utils.R /^gtable_remove_grob <- function(x, pattern, which = 1L, $/;" f
gtable_table R/gtables.R /^gtable_table <- function(d, widths, heights,$/;" f
gtables R/gtable_utils.R /^ gtables <- z_arrange_gtables(gtables, z)$/;" v
gtables R/gtable_utils.R /^ gtables <- list(...)$/;" v
height R/vectorgrobs.R /^ height = unit(100, "mm"), $/;" v
heights R/gtable_utils.R /^ heights = unit(rep(0, nrow(x)), "cm"), $/;" v
heights R/gtables.R /^ heights = heights, vp=vp)$/;" v
heights R/gtables.R /^ heights <- row_heights(frgds_grobs)$/;" v
heights R/test.R /^# lo <- graphics::layout(mat = mat.lo, heights = c(2, 12, ann.height, leg.height))$/;" v
heights tests/testthat/test-gtables.R /^ heights <- unit(4, "mm")$/;" v
hjust R/test.R /^# hjust = 1, x = 0.95),$/;" v
idx R/gtable_utils.R /^ idx <- switch(join,$/;" v
inner R/gtable_utils.R /^ inner = intersect(names_x, names_y),$/;" v
insert.unit R/gtable_utils.R /^insert.unit <- function (x, values, after = length(x)) {$/;" f
join R/gtable_utils.R /^align_2 <- function(x, y, along = 1L, join = "outer") {$/;" v
join R/gtable_utils.R /^combine <- function (..., along = 1L, join = "outer") {$/;" v
join R/gtable_utils.R /^combine_2 <- function(x, y, along = 1L, join = "outer") {$/;" v
join R/gtable_utils.R /^gtable_combine <- function (..., along = 1L, join = "outer") $/;" v
label R/vectorgrobs.R /^ label <- tryCatch(parse(text=label), $/;" v
last R/gtable_utils.R /^ last = y$heights,$/;" v
last R/gtable_utils.R /^ last = y$widths,$/;" v
layout.matrix R/test.R /^# layout.matrix <- matrix(data = c(1,2,3,4), nrow = 2, ncol = 2, byrow = TRUE)$/;" v
left R/gtable_utils.R /^ left = names_x,$/;" v
lineend R/vectorgrobs.R /^ lineend = "round", $/;" v
lineend R/vectorgrobs.R /^ lineend = "round", $/;" v
linejoin R/vectorgrobs.R /^ linejoin = "round", $/;" v
linejoin R/vectorgrobs.R /^ linejoin = "round", $/;" v
lty R/vectorgrobs.R /^ lty = "solid", $/;" v
lty R/vectorgrobs.R /^ lty = "solid", $/;" v
mat R/test.R /^# mat <- matrix(list(a, b, c, nullGrob()), nrow = 2)$/;" v
mat.lo R/test.R /^# mat.lo <- matrix(data = c(1,2,3), nrow = 3, ncol = 1, byrow = TRUE)$/;" v
mat.lo R/test.R /^# mat.lo <- matrix(data = c(1,2,3,4), nrow = 4, ncol = 1, byrow = TRUE)$/;" v
mat.lo R/test.R /^# mat.lo <- matrix(data = c(1,2,3,4,5,5), nrow = 3, ncol = 2, byrow = TRUE)$/;" v
mat.lo R/test.R /^# mat.lo <- matrix(data = c(1,2,3,4,5,6,7,7), nrow = 4, ncol = 2, byrow = TRUE)$/;" v
matches R/gtable_utils.R /^ matches <- grep(pattern, x$layout$name, fixed = fixed)$/;" v
max R/gtable_utils.R /^ max = unit.pmax(x$heights, y$heights))$/;" v
max R/gtable_utils.R /^ max = unit.pmax(x$widths, y$widths)$/;" v
median tests/testthat/testdata/DBS.R /^ "median" = "median mutations per Mb due to the signature")$/;" v
metadata tests/testthat/testdata/DBS.R /^ metadata = metadata$/;" v
metadata tests/testthat/testdata/DBS.R /^metadata <- list("proportion" = "Proportion of tumors with the signature",$/;" g
metadata tests/testthat/testdata/DEXP.R /^ metadata = metadata$/;" v
metadata tests/testthat/testdata/DEXP.R /^metadata <- list("pvalue" = "adjusted pvalue multiple testing",$/;" g
min R/gtable_utils.R /^ min = unit.pmin(x$heights, y$heights),$/;" v
min R/gtable_utils.R /^ min = unit.pmin(x$widths, y$widths),$/;" v
missing R/gtable_utils.R /^ missing <- setdiff(index, old_index)$/;" v
name R/gtables.R /^ name = "table", vp = NULL, ...){$/;" v
name R/vectorgrobs.R /^ name = name, vp = vp,$/;" v
name R/vectorgrobs.R /^ name = name, vp = vp,$/;" v
names_x R/gtable_utils.R /^ names_x <- dimnames(x)[[along]]$/;" v
names_y R/gtable_utils.R /^ names_y <- dimnames(y)[[along]]$/;" v
old_index R/gtable_utils.R /^ old_index <- switch(along, rownames(x), colnames(x))$/;" v
out tests/testthat/test-gtable_utils.R /^ out <- plot_grob(g, name="gtable_circle_cbind.pdf", width=10, height=6)$/;" v
out tests/testthat/test-gtable_utils.R /^ out <- plot_grob(g, name="gtable_rbind_2_text_circle.pdf")$/;" v
out tests/testthat/test-gtable_utils.R /^ out <- plot_grob(g, name="gtable_rbind_2_text_mat.pdf", width=4, height=3)$/;" v
out tests/testthat/test-gtable_utils.R /^ out <- plot_grob(g, name="gtable_rbind_2_text_row.pdf", width=4, height=1)$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(g, name="gtable_circle.pdf")$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(gc, name="gtable_text_row_no_padding.pdf", width=8, height=1)$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(gc, name="gtable_text_row_with_padding.pdf", width=8, height=1)$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(gr, name="gtable_text_col.pdf", width=1, height=4.5)$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(gr, name="gtable_text_mat_no_padding.pdf")$/;" v
out tests/testthat/test-gtables.R /^ out <- plot_grob(gr, name="gtable_text_mat_with_padding.pdf")$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob.pdf", width=4, height=4)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_cols_more.pdf", width=4, height=4)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_cols_more_rows_more_no_color.pdf", width=5, height=4)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_cols_more_rows_more_with_color.pdf", width=5, height=4)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_genes.pdf", width=5, height=12)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_genes_dmin_dmax.pdf", width=5, height=12)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_genes_dmin_dmax_with_scale_breaks.pdf", width=5, height=12)$/;" v
out tests/testthat/test-table_extra_grob.R /^ out <- plot_grob(g, name="table_extra_grob_pcawg.pdf", width=12, height=16)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="circle_grob.pdf", width=1, height=1)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="rect_circle_grob.pdf", width=1, height=1)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="rect_circle_grob_small.pdf", width=4, height=4)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="rect_grob.pdf", width=1, height=1)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="rect_grob_xy.pdf", width=1, height=1)$/;" v
out tests/testthat/test-vectorgrobs.R /^ out <- plot_grob(g, name="text_grob.pdf", width=1, height=1)$/;" v
outer R/gtable_utils.R /^ outer = union(names_x, names_y)$/;" v
padding R/gtables.R /^ padding = unit(c(4, 4), "mm"),$/;" v
padding R/test.R /^# padding = unit(c(4, 4), "mm"), ...){$/;" v
padding R/test.R /^# padding = padding)$/;" v
padding R/test.R /^# padding = padding)$/;" v
params R/table_params.R /^ params <- c(params_scale, params_color)$/;" v
params R/table_params.R /^ params <- list(fill=as.vector(d))$/;" v
params R/table_params.R /^ params <- params_scale$/;" v
params R/table_params.R /^ params <- list(label=d)$/;" v
params R/table_params.R /^ params <- list(r=do.call(unit.c, lapply(d, r_func)))$/;" v
params_color R/table_params.R /^ params_color <- table_params_circle_color(d=dcolor, color_palette=color_palette, color_breaks=color_breaks)$/;" v
params_scale R/table_params.R /^ params_scale <- table_params_circle_scale(d=dscale, scale_breaks=scale_breaks, r_min=r_min, r_max=r_max, $/;" v
plot_grob tests/testthat/helper.R /^plot_grob <- function(g, name, width=NULL, height=NULL){$/;" f
r_func R/table_params.R /^ r_func <- function(x){$/;" f
rbind_2 R/gtable_utils.R /^rbind_2 <- function(x, y, size = "max", height=NULL) {$/;" f
rect_grob R/vectorgrobs.R /^rect_grob <- function(fill = "white", $/;" f
rep_along R/other_utils.R /^rep_along <- function(x, y) {$/;" f
rep_ifshort R/other_utils.R /^rep_ifshort <- function(x, n, nc, nr){$/;" f
right R/gtable_utils.R /^ right = names_y, $/;" v
rot R/vectorgrobs.R /^ rot = rot, check.overlap = check.overlap, $/;" v
row R/test.R /^# row <- matrix(list(a, b, c), nrow = 1)$/;" v
rowData tests/testthat/testdata/DBS.R /^ rowData = rowData,$/;" v
rowData tests/testthat/testdata/DBS.R /^rowData <- data.frame(name=rows, description=rows.desc, stringsAsFactors=F)$/;" g
rowData tests/testthat/testdata/DEXP.R /^ rowData = rowData,$/;" v
rowData tests/testthat/testdata/DEXP.R /^rowData <- data.frame(name=rows, stringsAsFactors=F)$/;" g
row_heights R/other_utils.R /^row_heights <- function(m){$/;" f
rowhead R/test.R /^# rowhead <- list(fg_fun = text_grob, $/;" v
rowhead R/theme_awesome.R /^ rowhead <- list(fg_fun=text_grob, $/;" v
rowmore R/theme_awesome.R /^ rowmore <- list(fg_fun=text_grob, $/;" v
rownames R/gtable_utils.R /^ rownames = missing)$/;" v
rows R/table_extra_grob.R /^ rows <- c("", names(cols_more), rows)$/;" v
rows R/table_extra_grob.R /^ rows <- c("", rows)$/;" v
rows R/test.R /^# rows = rownames(DBS),$/;" v
rows tests/testthat/testdata/DBS.R /^rows <- sapply(1:11, function(i) paste0("DBS",i))$/;" g
rows tests/testthat/testdata/DEXP.R /^rows <- sapply(1:50, function(i) paste0("ENSG00000",i))$/;" g
rows.desc tests/testthat/testdata/DBS.R /^rows.desc <- c("Ultraviolet light exposure", "Tobacco Smokin and other", "POLE mutation", "", "Platinum treatment", "",$/;" g
rows_m R/table_extra_grob.R /^ rows_m <- c("", names(rows_more), rows_more[[rows_m_name]])$/;" v
rows_m R/table_extra_grob.R /^ rows_m <- c("", rows_more[[rows_m_name]])$/;" v
rows_more tests/testthat/test-table_extra_grob.R /^ rows_more <- list("Proposed aetiology"=SummarizedExperiment::rowData(DBS)$description)$/;" v
scale_breaks tests/testthat/test-table_extra_grob.R /^ scale_breaks <- c(1, 2, 5)$/;" v
size R/gtable_utils.R /^ Reduce(function(x, y) cbind_2(x, y, size = size), gtables)$/;" v
size R/gtable_utils.R /^ Reduce(function(x, y) rbind_2(x, y, size = size), gtables)$/;" v
size R/gtable_utils.R /^cbind_2 <- function(x, y, size = "max", width=NULL) {$/;" v
size R/gtable_utils.R /^gtable_cbind <- function(..., size = "max", z = NULL) {$/;" v
size R/gtable_utils.R /^gtable_rbind <- function(..., size = "max", z = NULL) {$/;" v
size R/gtable_utils.R /^rbind_2 <- function(x, y, size = "max", height=NULL) {$/;" v
table_extra_grob R/table_extra_grob.R /^table_extra_grob <- function(dscale, dcolor=NULL,$/;" f
table_params R/table_params.R /^table_params <- function(d, fg_params, bg_params){$/;" f
table_params_circle R/table_params.R /^table_params_circle <- function(dscale, dcolor, scale_breaks, r_min, r_max, color_palette, color_breaks, $/;" f
table_params_circle_color R/table_params.R /^table_params_circle_color <- function(d, color_palette, color_breaks=NULL){$/;" f
table_params_circle_scale R/table_params.R /^table_params_circle_scale <- function(d, scale_breaks=10, r_min=unit(4, "mm"), r_max=unit(10, "mm"), d_min=NULL, $/;" f
table_params_text R/table_params.R /^table_params_text <- function(d){$/;" f
tb_params R/gtables.R /^ tb_params <- table_params(d, fg_params, bg_params)$/;" v
text_grob R/vectorgrobs.R /^text_grob <- function(label, $/;" f
theme tests/testthat/test-gtable_utils.R /^ theme <- ttheme_awesome()$/;" v
theme tests/testthat/test-gtables.R /^ theme <- ttheme_awesome()$/;" v
theme tests/testthat/test-gtables.R /^ theme <- ttheme_awesome(padding=unit(c(0,0), "mm"))$/;" v
theme tests/testthat/test-gtables.R /^ theme <- ttheme_awesome(padding=unit(c(1,1), "mm"))$/;" v
theme tests/testthat/test-gtables.R /^ theme <- ttheme_awesome(padding=unit(c(2,0), "mm"))$/;" v
theme tests/testthat/test-table_extra_grob.R /^ theme <- ttheme_awesome(base_size=12,$/;" v
theme tests/testthat/test-table_extra_grob.R /^ theme <- ttheme_awesome(core_size=unit(5, "mm"))$/;" v
theme tests/testthat/test-table_extra_grob.R /^ theme <- ttheme_awesome(core_size=unit(5, "mm"), $/;" v
theme tests/testthat/test-table_extra_grob.R /^ theme <- ttheme_awesome(core_size=unit(5, "mm"), color_palette=color_palette, color_breaks=color_breaks)$/;" v
ties.method R/gtable_utils.R /^ x$layout$z <- rank(x$layout$z, ties.method = "first") + i - $/;" v
tokeep R/gtable_utils.R /^ tokeep <- setdiff(seq_len(length(x)), matches[which])$/;" v
ttheme_awesome R/theme_awesome.R /^ttheme_awesome <- function(base_size=8, $/;" f
width R/vectorgrobs.R /^ width = unit(100, "mm"), $/;" v
widths R/gtable_utils.R /^ widths = unit(rep(0, ncol(x)), "cm"), $/;" v
widths R/gtables.R /^ widths = widths, $/;" v
widths R/test.R /^# lo <- graphics::layout(mat = mat.lo, heights = c(12, ann.height, leg.height), widths = c(6, 1))$/;" v
widths R/test.R /^# lo <- graphics::layout(mat = mat.lo, widths = c(6, 1), heights = c(2, 12, 1, leg.height))$/;" v
x R/gtable_utils.R /^ x <- cbind(x, spacer, size = "first")$/;" v
x R/gtable_utils.R /^ x <- rbind(x, spacer, size = "first")$/;" v
x R/gtable_utils.R /^ x <- gtable::gtable_add_cols(x, width)$/;" v
x R/gtable_utils.R /^ x <- gtable::gtable_add_rows(x, height)$/;" v
x R/gtable_utils.R /^ x <- gtable_trim(x)$/;" v
x R/gtable_utils.R /^ x = gtable_reindex(x, idx, along), $/;" v
x R/vectorgrobs.R /^ x = unit(0.5, "npc"), $/;" v
x R/vectorgrobs.R /^ x = unit(0.5, "npc"), $/;" v
x R/vectorgrobs.R /^ textGrob(label = label, x = x, y = y, $/;" v
y R/gtable_utils.R /^ y = gtable_reindex(y, idx, along)$/;" v
y R/vectorgrobs.R /^ y = unit(0.5, "npc"),$/;" v
y R/vectorgrobs.R /^ y = unit(0.5, "npc"),$/;" v
z R/test.R /^# z <- matrix(c(3, 1, 2, 4), nrow = 2)$/;" v
z_arrange_gtables R/gtable_utils.R /^z_arrange_gtables <- function (gtables, z) $/;" f
z_normalise R/gtable_utils.R /^z_normalise <- function (x, i = 1) $/;" f
zmax R/gtable_utils.R /^ zmax <- max(gtables[[i]]$layout$z)$/;" v
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