create.diagram: Create a diagram object.

In lemna/ugir: Functions for registry-based cancer research

Description

This function creates a diagram object, which contains a diagram statement for use by the grViz function and vectors of from and to nodes.

Usage

create.diagram(flowchart, preamble = "digraph {\nnode[shape=box, fontname = Helvetica]")

Arguments

flowchart	A flowchart dataframe, as produced by the create.flowchart and add.node functions
preamble	preamble used by the grViz function

Details

See the documentation for grViz for preamble options.

Value

A list containing the following items:

diagram	a diagram statement for use by grViz
from.nodes	a character vector containing from node descriptions
to.nodes	a character vector containing to node descriptions

Author(s)

Peter Konings

See Also

create.flowchart creates an empty flowchart dataframe for use by this function. add.node adds one or two nodes as row(s) to this type of dataframe.

Examples

# create an empty flowchart dataframe
testchart <- create.flowchart()

# create a test dataframe and add it to the flowchart
testdf <- data.frame(lpnr = c(1,1,1,1:10), blah = rep('blah', 13))
testchart <- add.node(testdf, testchart,  'start', 'original dataset')

# create a second test dataframe and add it to the flowchart
cancertest <- data.frame(lpnr = 1:8, cancer = c(rep('benign', 4), rep('bad', 4)))
testchart <- add.node(cancertest, testchart, 'cancerstart', 'cancer registry')

# remove duplicate records from the test dataframe, add it to the flowchart
testdf <- unique(testdf)
testchart <- add.node(testdf, testchart, 'unique', 'unique records', from = 'start')

# split the test dataframe, add results to the flowchart
testdf1 <- testdf[1:5,]
testdf2 <- testdf[6:10,]
testchart <- add.node(testdf1, testchart, 'first5', 'first five records',
  from = 'unique', display.r = FALSE)
testchart <- add.node(testdf2, testchart, 'last5', 'last five records',
  from = 'unique', display.r = FALSE)

# merge two dataframes, add to flowchart
testdf1 <- merge(testdf1, cancertest, by = 'lpnr', all.x = FALSE, all.y = FALSE)
testchart <- add.node(testdf1, testchart, 'benigncases', 'benign cases',
                      from = c('cancerstart', 'first5'))


testdf2 <- merge(testdf2, cancertest, by = 'lpnr', all.x = FALSE, all.y = FALSE)
testchart <- add.node(testdf2, testchart, 'badcases', 'malignant cases',
                      from = c('cancerstart', 'last5'),display.r = FALSE)

# create yet another dataframe, unconnected to anything else
unconnecteddf <- data.frame(lpnr = c(1:5), blah = rep('blah', 5))
testchart <- add.node(unconnecteddf, testchart, 'unconnected', 'unconnected dataset')


# show the final flowchart dataframe
testchart

# create a diagram statement from the flowchart dataframe and visualize it
my.diagram <- create.diagram(testchart)
from.nodes <- my.diagram$from.nodes
to.nodes <- my.diagram$to.nodes
grViz(my.diagram$diagram)

lemna/ugir documentation built on May 21, 2019, 3:07 a.m.