comparison w4mcorcov_output.R @ 5:50f60f94c034 draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
author eschen42
date Fri, 30 Mar 2018 14:59:19 -0400
parents 23f9fad4edfc
children
comparison
equal deleted inserted replaced
4:8bba31f628da 5:50f60f94c034
1
2 # turn off all plotting devices
3 dev.off.all <- function() {
4 while (!is.null(dev.list())) { dev.off() }
5 }
6
7 # capture plot and write to PDF; then close any devices opened in the process
8 plot2pdf <- function(
9 file.name
10 , plot.function
11 , width = 12
12 , height = 12
13 ) {
14 # capture plot and write to PDF
15 cur.dev <- dev.list()
16 filename <- file.name
17 pdf(file = filename, width = width, height = height)
18 plot.function()
19 # close any devices opened in the process
20 dev.off()
21 if (is.null(cur.dev)) {
22 dev.off.all()
23 } else {
24 while ( length(dev.list()) > length(cur.dev) ) { dev.off() }
25 }
26 }
27
28 # print and capture plot and write to PDF; then close any devices opened in the process
29 # This is needed for ggplot which does not print the plot when invoked within a function.
30 print2pdf <- function(
31 file.name
32 , plot.function
33 , width = 12
34 , height = 12
35 ) {
36 plot2pdf(
37 file.name = file.name
38 , width = width
39 , height = height
40 , plot.function = function() {
41 print(plot.function())
42 }
43 )
44 }
45
46 iso8601.znow <- function()
47 {
48 strftime(as.POSIXlt(Sys.time(), "UTC"), "%Y-%m-%dT%H:%M:%SZ")
49 }
50
51 # pdf.name <- function(name)
52 # {
53 # paste0(name, "_", iso8601.filename.fragment(), ".pdf")
54 # }
55 #
56 # tsv.name <- function(name)
57 # {
58 # paste0(name, "_", iso8601.filename.fragment(), ".tsv")
59 # }
60 #
61
62 tsv_action_factory <- function(file, colnames, append) {
63 return (
64 function(tsv) {
65 write.table(
66 x = tsv
67 , file = file
68 , sep = "\t"
69 , quote = FALSE
70 , row.names = FALSE
71 , col.names = colnames
72 , append = append
73 )
74 }
75 )
76 }
77