Mercurial > repos > bcclaywell > microbiome_community_suite

annotate ribbonPlot.R @ 0:12b4f093e6c4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
1 #!/usr/bin/env Rscript
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
2
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
3 ## begin warning handler
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
4 withCallingHandlers({
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
5
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
6 library(methods) # Because Rscript does not always do this
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
7
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
8 options('useFancyQuotes' = FALSE)
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
9
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
10 suppressPackageStartupMessages(library("optparse"))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
11 suppressPackageStartupMessages(library("RGalaxy"))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
12
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
13
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
14 option_list <- list()
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
15
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
16 option_list$CommunityFile <- make_option('--CommunityFile', type='character')
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
17 option_list$Attributes <- make_option('--Attributes', type='character')
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
18 option_list$ClusteringAlgorithm <- make_option('--ClusteringAlgorithm', type='character')
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
19 option_list$OutputFile <- make_option('--OutputFile', type='character')
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
20
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
21
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
22 opt <- parse_args(OptionParser(option_list=option_list))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
23
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
24 suppressPackageStartupMessages(library(microbiomePkg))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
25
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
26 ## function body not needed here, it is in package
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
27
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
28 params <- list()
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
29 for(param in names(opt))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
30 {
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
31 if (!param == "help")
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
32 params[param] <- opt[param]
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
33 }
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
34
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
35 setClass("GalaxyRemoteError", contains="character")
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
36 wrappedFunction <- function(f)
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
37 {
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
38 tryCatch(do.call(f, params),
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
39 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
40 }
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
41
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
42
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
43 suppressPackageStartupMessages(library(RGalaxy))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
44 do.call(ribbonPlot, params)
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
45
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
46 ## end warning handler
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
47 }, warning = function(w) {
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
48 cat(paste("Warning:", conditionMessage(w), "\n"))
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
49 invokeRestart("muffleWarning")
12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
bcclaywell
parents:
diff changeset
50 })