Step title

Show a title given to the step.

Add a line or table of used filters in a given step. Since a step should probably come from a YAML file, then it'll iteratively look for filtering, filters, filter, in that order. Lastly, it looks for subset.

Show parameters used for a step.

Show tables with DT::datatable or knitr::kable.

Add description from a step element.

Connect google document.

Show step's issues.

Show step's command(s).

Create step's section.

report_title(x, conf, hlevel = "###")

report_filters(x)

report_parameters(x)

report_tables(x, interactive = "choose", table_summarise = FALSE)

report_description(x, conf = NULL, hide = FALSE)

report_gsheet(x)

report_issues(x, name = "", hlevel = "###")

report_command(x, type = "bash")

report_section(
  object,
  name = 1,
  hide = FALSE,
  lock = FALSE,
  hlevel = "###",
  close_tabset = FALSE
)

Arguments

x	Step's config.
conf	Step's arguments, Default: NULL.
hlevel	Header level, Default: '###'.
interactive	Use DT?, Default: 'choose' (if No. of rows > 15).
table_summarise	Make a summary of the table, Default: FALSE.
hide	Collapsible description, Default: FALSE.
name	Step's name, Default: 1.
type	Type of chunk (r, bash, python).
object	Reportr object.
lock	Is it a step with "locked" parameters, Default: FALSE.
close_tabset	In case you need something to show right after the last tab, Default: FALSE.

Value

Prints the title using cat.

None (invisible 'NULL'). If one filter it will show a line, if not it will use 'knitr::kable' after reshape2::melt.

Prints a kable.

Creates a table.

Prints the description.

Prints an iframe object.

Prints the issues (if found).

Prints the command into a selected chunk type.

Prints all the elements of a step.

Details

It accepts a single filtering criteria or multiple (melted).

It accepts a list, looks for "lock" or "parameters" and takes the first one it finds.

Creates a temporary Rmd file and calls it with knit_child.

Examples

if (FALSE) {
 if(interactive()) {
  report_title(x = "Step N", conf = list("~/Documents/liai/literature"))
 }
}
if (FALSE) {
  if(interactive()){
    report_filters(x = list(filtering = "n_umi >= 1000"))
  }
}
if (FALSE) {
  if(interactive()) report_parameters(list(parameters = NULL))
}
if (FALSE) {
 if(interactive()) {
  report_tables(x = "~/Documents/liai/asthma/biopsy/metadata_library.csv")
 }
}
if (FALSE) {
 if(interactive()){
  report_description("Description")
  report_description(list(description = "Brief description"))
  report_description("Description", hide = TRUE)
 }
}
if (FALSE) {
 if(interactive()) {
  report_gsheet("spreadsheets/d/1v3ff8KKWGK5iCAyMa0v45wiw5El4Lcy0HVjTAbuYguU")
 }
}
if (FALSE) {
 if(interactive()) {
  report_issues(list(issues = "Red is not a colour"))
  report_issues(list(issues = "Solved: red _is_ a colour"))
  report_issues(list(issues = "Fatal: red _is_ blue!"))
 }
}
if (FALSE) {
 if(interactive()) report_command(list(command = "sh /path/to/script.sh"))
}
if (FALSE) {
 if(interactive()) {
  mysteps = list(s1 = list("~/Documents/liai/literature", issues = "Oh no!"))
  mysteps$s1$hfiles = c(`Cool review` = "immunology.pdf")
  ws = create_wsteps(mysteps)
  report_section(ws)
 }
}

Arguments

Value

Details

See also

Examples