learn_theme_label.Rdlearn label paramters as list
learn_theme_label(lines, sep)a vector of character strings from template file.
a character specifying the separator.
a list of label parameters containing
1/0 specifying display or hide the text labels above each field column
a number specifying the size factor for the text labels
1/0 specifying the labels position. If 0, label text which does not fit into the shape will be hidden
1/0 specifying the labels position. By default, internal labels will be placed above the branches. If 1, labels will be below the branches
a number specifying text label rotation angle
1/0 specifying tree rotation. If set to 1, tree rotation will not influence the individual label rotation
a number specifying the label vertical shift. Shift internal labels vertically by this amount of pixels (positive or negative)
a number specifying the label shift. text label shift in pixels (positive or negative)
1/0 specifying label external shift that add extra horizontal shift to the external labels. Useful in unrooted display mode to shift text labels further away from the node labels.
library(dplyr)
#> Warning: package ‘dplyr’ was built under R version 4.2.3
#>
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#>
#> filter, lag
#> The following objects are masked from ‘package:base’:
#>
#> intersect, setdiff, setequal, union
tree <- system.file("extdata",
"tree_of_itol_templates.tree",
package = "itol.toolkit")
tab_tmp <- data.table::fread(system.file("extdata",
"parameter_groups.txt",
package = "itol.toolkit"))
tab_id_group <- tab_tmp[,c(1,2)]
tab_tmp <- tab_tmp[,-c(1,2)]
tab_tmp_01 <- convert_01(object = tab_tmp)
tab_tmp_01 <- cbind(tab_id_group,tab_tmp_01)
order <- c("type","separator","profile","field","common themes",
"specific themes","data")
tab_tmp_01_long <- tab_tmp_01 %>%
tidyr::gather(key = "variable",
value = "value",
c(-parameter,-group))
template_start_group <- tab_tmp_01_long %>%
group_by(group,variable) %>%
summarise(sublen = sum(value)) %>%
tidyr::spread(key=variable,
value=sublen)
#> `summarise()` has grouped output by 'group'. You can override using the
#> `.groups` argument.
template_start_group$group <- factor(template_start_group$group,
levels = order)
template_start_group <- template_start_group %>% arrange(group)
start_group <- data.frame(Var1 = template_start_group$group,
Freq = apply(template_start_group[,-1], 1, max))
start_group$start <- 0
for (i in 2:nrow(start_group)) {
start_group$start[i] <- sum(start_group$Freq[1:(i-1)])
}
template_start_group[template_start_group == 0] <- NA
template_end_group <- template_start_group[,2:(ncol(template_start_group)-1)] + start_group$start
template_end_group <- data.frame(group = order,template_end_group)
template_end_group_long <- template_end_group %>%
tidyr::gather(key = "variable",
value = "value",
-group)
names(template_end_group_long)[3] <- "end"
template_end_group_long$start <- rep(start_group$start,
length(unique(template_end_group_long$variable)))
template_end_group_long <- template_end_group_long %>% na.omit()
template_end_group_long$length <- sum(start_group$Freq)
template_end_group_long <- template_end_group_long[,c(2,5,4,3,1)]
template_end_group_long$group <- factor(template_end_group_long$group,levels = order)
unit <- create_unit(data = template_end_group_long,
key = "Quickstart",
type = "DATASET_DOMAINS",
tree = tree)
#> Using the first column as id: variable
#> Using following column as length parameter: length
#> Using following column as start parameter: start
#> Using following column as end parameter: end
#> Identifying data column to auto setup color parameter
#> Using default color pattern: table2itol
#> Identifying data column to auto setup shape parameter
file <- tempfile()
write_unit(unit,file)
lines <- line_clean(file=file)
sep = learn_separator(file = file)
learn_theme_label(lines,sep)
#> $display
#> NULL
#>
#> $size
#> NULL
#>
#> $top
#> [1] "0"
#>
#> $below
#> NULL
#>
#> $rotation
#> NULL
#>
#> $straight
#> NULL
#>
#> $vertical
#> NULL
#>
#> $shift
#> NULL
#>
#> $external_shift
#> NULL
#>