Build a pipeline lineage graph from the active session

Constructs a visual representation of the full pipeline : every tagged dataset, every lg_derive(), lg_join(), and lg_filter() operation, and every exclusion branch : as a list of nodes and edges with a Graphviz DOT string.

Usage

lg_lineage(rankdir = c("TB", "LR"))

Arguments

rankdir: Character. Layout direction: "TB" (top to bottom, default) or "LR" (left to right).

Value

An lg_lineage object (list) with components:

nodes: Named list of node metadata.
edges: Named list of edge metadata.
dot: Character string. Graphviz DOT representation.
rankdir: The layout direction used.

Details

Render with lg_plot() for inline display in RStudio or a knitr document, or write the DOT string to a file and render externally with Graphviz.

Examples

lg_start()
#> lineager: session started
patients <- data.frame(
  USUBJID  = c("P01","P02","P03","P04","P05"),
  eligible = c(TRUE, FALSE, TRUE, TRUE, FALSE),
  age      = c(34L, 17L, 52L, 29L, 61L),
  stringsAsFactors = FALSE
)
pts <- lg_tag(patients, dataset_id = "PATIENTS")
#> lineager: tagged 'PATIENTS' — 5 rows, 3 cols
pts <- lg_derive(pts, adult = age >= 18L,
                 description = "adult flag from age")
#> lineager: [PATIENTS] derive — adult flag from age
lg_filter(pts, eligible & adult,
          reason = "Ineligible or under 18")
#> lineager: [PATIENTS] filter 'Ineligible or under 18' — 5 in, 3 out, 2 excluded
#> <lg_df> 'PATIENTS'  [3 × 5]
#>   USUBJID eligible age adult
#> 1     P01     TRUE  34  TRUE
#> 2     P03     TRUE  52  TRUE
#> 3     P04     TRUE  29  TRUE

lin <- lg_lineage()
print(lin)
#> <lg_lineage>  1 source dataset(s), 2 operation(s), 1 exclusion branch(es)
#> Use lg_plot(lin) to render. DOT source:
#> 
#> digraph lineage {
#>   rankdir = TB;
#>   graph [fontname="Helvetica", splines=ortho, nodesep=0.4, ranksep=0.6];
#>   node  [fontname="Helvetica", fontsize=10, margin="0.15,0.08"];
#>   edge  [fontname="Helvetica", fontsize=9, color="#6b6f80"];
#> 
#>   SRC_PATIENTS [label="PATIENTS\nn = 5", shape=box, style="filled,rounded", fillcolor="#e8effe", color="#1a56db", fontcolor="#0f1117"];
#>   OP_op_0001 [label="DERIVE\nadult flag from age", shape=ellipse, style="filled,rounded", fillcolor="#fff8e1", color="#f59e0b", fontcolor="#0f1117"];
#>   DS_PATIENTS_op_0001 [label="PATIENTS\nn = 5", shape=box, style="filled,rounded", fillcolor="#ffffff", color="#6b6f80", fontcolor="#0f1117"];
#>   OP_op_0002 [label="FILTER\nIneligible or under 18\n−2 rows", shape=ellipse, style="filled,rounded", fillcolor="#fff3e0", color="#ea8c00", fontcolor="#0f1117"];
#>   DS_PATIENTS_op_0002 [label="PATIENTS\nn = 3", shape=box, style="filled,rounded", fillcolor="#ffffff", color="#6b6f80", fontcolor="#0f1117"];
#>   EXCL_op_0002 [label="excluded\nn = 2", shape=plaintext, fontcolor="#dc2626", fontsize=9];
#> 
#>   SRC_PATIENTS -> OP_op_0001;
#>   OP_op_0001 -> DS_PATIENTS_op_0001;
#>   DS_PATIENTS_op_0001 -> OP_op_0002 [label=" n=5 "];
#>   OP_op_0002 -> DS_PATIENTS_op_0002;
#>   OP_op_0002 -> EXCL_op_0002;
#> } 
lg_end()
#> lineager: session ended — 2 operation(s), 2 exclusion(s), 0 population(s), 0 var spec(s)