plotWF: Visualize SPR workflow and status

Description Usage Arguments Details Value

View source: R/plotwf.R

Description

Visualize SPR workflow and status

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
plotWF(
  sysargs,
  width = NULL,
  height = NULL,
  elementId = NULL,
  responsive = TRUE,
  branch_method = "auto",
  branch_no = NULL,
  layout = "compact",
  no_plot = FALSE,
  plot_method = "svg",
  out_format = "plot",
  out_path = NULL,
  show_legend = TRUE,
  mark_main_branch = TRUE,
  rstudio = FALSE,
  in_log = FALSE,
  rmarkdown = "detect",
  verbose = FALSE,
  exit_point = 0
)

Arguments

sysargs

The workflow structure dataframe

width

string, a valid CSS string for width, like "500px", "100%"

height

string, a valid CSS string for height, like "500px", "100%"

elementId

string, optional ID value for the plot

responsive

bool, should the plot be responsive? useful in Rstudio built-in viewer, Rmarkdown, Shiny or embed it into other web pages.

branch_method

string, one of "auto", "choose". How to determine the main branch of the workflow. "auto" will be determined by internal alrgothrim: Branches connecting the frist and last step and/or the longest will be favored. "choose" will list all possible branches and you can make a choice.

branch_no

numeric, only works if branch_method == "choose". Specify a branch number to be the main branch instead of choosing from the prompt. This option can be good if you are in a non-interactive mode, e.g. rendering Rmd.

layout

string, one of "compact", "vertical", "horizontal", "execution"

no_plot

bool, if you want to assgin the plot to a variable and do not want to see it interactively, change this to FALSE

plot_method

string, one of "svg", "png", how to make plot, use svg or png to embed the plot.

out_format

string, one of "plot", "html", "dot", "dot_print"

  • plot: directly open your viewer or browser of the plot

  • html: save the plot to a html file

  • dot: save the plot in DOT language, need a dot engine to remake the plot

  • dot_print: directly cat the DOT code on console

out_path

string, if the out_format is not "plot" or "dot_print", provide a path of where to save the plot.

show_legend

bool, show plot legend?

mark_main_branch

bool, color the main branch on the plot?

rstudio

bool, if you are using Rstudio, open the built-in viewer to see the plot? Default is no, open the browser tab to see it plot. The default viewer is too small to see the full plot clearly, so we recommend to use the broswer tab.

in_log

bool, is this plot been made in a SPR log file? If TRUE will add links of steps to the corresponding log sections.

rmarkdown

are you rendering this plot in a Rmarkdown document? default value is "detect", this function will determine based on current R environment, or you can force it to be TRUE or FALSE

verbose

bool, turn on verbose mode will give you more information

exit_point

numeric, for advanced debugging only, see details

Details

layout

exit_point

return intermediate results at different points and exit the function

Rmarkdown

Rmarkdown will change some of the format and cause conflicts. If the plot can be rendered outside Rmd but cannot within Rmd, try to turn this option on. Some additional javascript processing will be performed to avoid the conflict but may cause unknown issues.

Value

see out_format and exit_point


tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.