cummerbund: test-data/maplot.txt annotate

annotate test-data/maplot.txt @ 4:ba8fde59843d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

author	devteam
date	Tue, 21 Jul 2015 14:18:39 -0400
parents	587c425b4e76
children	78fcfc04fcfe

rev	line source
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	1
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	3 Copyright (C) 2014 The R Foundation for Statistical Computing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	4 Platform: x86_64-unknown-linux-gnu (64-bit)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	5
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	6 R is free software and comes with ABSOLUTELY NO WARRANTY.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	7 You are welcome to redistribute it under certain conditions.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	8 Type 'license()' or 'licence()' for distribution details.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	9
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	10 Natural language support but running in an English locale
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	11
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	12 R is a collaborative project with many contributors.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	13 Type 'contributors()' for more information and
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	14 'citation()' on how to cite R or R packages in publications.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	15
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	16 Type 'demo()' for some demos, 'help()' for on-line help, or
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	17 'help.start()' for an HTML browser interface to help.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	18 Type 'q()' to quit R.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	19
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	20 > ## Feature Selection ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	21 > get_features <- function(myGenes, f="gene") {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	22 + if (f == "isoforms")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	23 + return(isoforms(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	24 + else if (f == "tss")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	25 + return(TSS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	26 + else if (f == "cds")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	27 + return(CDS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	28 + else
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	29 + return(myGenes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	30 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	31 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	32 > ## Main Function ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	33 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	34 > library(argparse)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	35 Loading required package: proto
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	36 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	37 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	38 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	54 > parser$add_argument('--features', dest='features', action="store", default="genes")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	56 > parser$add_argument('--iter_max', dest='iter_max', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	57 > parser$add_argument('--genes', dest='genes', action="append")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	58 > parser$add_argument('--k', dest='k', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	59 > parser$add_argument('--x', dest='x', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	60 > parser$add_argument('--y', dest='y', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	61 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	62 > args <- parser$parse_args()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	63 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	64 > print(args)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	65 $border
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	66 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	67
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	68 $clustering
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	69 [1] "both"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	70
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	71 $count
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	72 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	73
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	74 $error_bars
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	75 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	76
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	77 $features
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	78 [1] "genes"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	79
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	80 $filename
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	81 [1] "plot-maplot-0.png"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	82
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	83 $gene_selector
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	84 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	85
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	86 $genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	87 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	88
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	89 $height
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	90 [1] 960
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	91
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	92 $input_database
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	93 [1] "/tmp/tmpk0xwrM/tmpNNuxXE/database/files/000/dataset_1.dat"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	94
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	95 $iter_max
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	96 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	97
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	98 $k
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	99 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	100
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	101 $labcol
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	102 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	103
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	104 $labrow
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	105 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	106
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	107 $log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	108 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	109
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	110 $plotType
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	111 [1] "maplot"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	112
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	113 $replicates
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	114 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	115
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	116 $smooth
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	117 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	118
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	119 $summary
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	120 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	121
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	122 $width
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	123 [1] 1280
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	124
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	125 $x
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	126 [1] "q1"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	127
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	128 $y
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	129 [1] "q2"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	130
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	131 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	132 > #q()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	133 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	134 > ## Load cummeRbund library
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	135 > library("cummeRbund")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	136 Loading required package: BiocGenerics
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	137 Loading required package: parallel
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	138
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	139 Attaching package: ‘BiocGenerics’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	140
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	141 The following objects are masked from ‘package:parallel’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	142
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	144 clusterExport, clusterMap, parApply, parCapply, parLapply,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	145 parLapplyLB, parRapply, parSapply, parSapplyLB
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	146
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	147 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	148
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	149 xtabs
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	150
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	151 The following objects are masked from ‘package:base’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	152
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	157 rownames, sapply, setdiff, sort, table, tapply, union, unique,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	158 unlist, unsplit
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	159
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	160 Loading required package: RSQLite
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	161 Loading required package: DBI
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	162 Loading required package: ggplot2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	163 Loading required package: reshape2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	164 Loading required package: fastcluster
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	165
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	166 Attaching package: ‘fastcluster’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	167
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	168 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	169
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	170 hclust
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	171
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	172 Loading required package: rtracklayer
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	173 Loading required package: GenomicRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	174 Loading required package: S4Vectors
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	175 Loading required package: stats4
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	176 Loading required package: IRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	177 Loading required package: GenomeInfoDb
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	178 Loading required package: Gviz
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	179 Loading required package: grid
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	180
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	181 Attaching package: ‘cummeRbund’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	182
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	183 The following object is masked from ‘package:GenomicRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	184
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	185 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	186
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	187 The following object is masked from ‘package:IRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	188
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	189 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	190
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	191 The following object is masked from ‘package:BiocGenerics’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	192
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	193 conditions
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	194
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	195 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	196 > ## Initialize cuff object
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	198 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	199 > ## Print out info
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	200 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	201 CuffSet instance with:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	202 2 samples
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	203 87 genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	204 90 isoforms
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	205 88 TSS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	206 0 CDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	207 87 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	208 88 splicing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	209 0 relCDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	210 > sink("cuffdb_info.txt")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	211 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	212 > print("SAMPLES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	213 > samples(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	214 > print("REPLICATES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	215 > replicates(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	216 > print("FEATURES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	217 > print(annotation(genes(cuff)))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	218 > cat(annotation(genes(cuff))[[1]],sep=",")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	219 > sink()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	220 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	222 > tryCatch({
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	223 + if (args$plotType == 'density') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	225 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	226 + else if (args$plotType == 'boxplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	228 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	229 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	230 + MDSplot(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	231 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	232 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	234 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	235 + else if (args$plotType == 'dendrogram') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	236 + csDendro(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	237 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	238 + else if (args$plotType == 'scatter') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	239 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	240 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	242 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	243 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	245 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	246 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	247 + else if (args$plotType == 'volcano') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	248 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	250 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	251 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	252 + myGenes <- genes(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	253 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	254 + csVolcano(myGenes, args$x, args$y)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	255 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	256 + else if (args$plotType == 'heatmap') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	257 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	258 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	259 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	260 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	262 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	264 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	265 + else if (args$plotType == 'cluster') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	266 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	267 + csCluster(get_features(myGenes, args$features), k=args$k)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	268 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	269 + else if (args$plotType == 'dispersion') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	270 + dispersionPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	271 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	272 + else if (args$plotType == 'fpkmSCV') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	273 + fpkmSCVPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	274 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	275 + else if (args$plotType == 'scatterMatrix') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	276 + csScatterMatrix(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	277 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	278 + else if (args$plotType == 'expressionplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	279 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	281 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	282 + else if (args$plotType == 'expressionbarplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	283 + myGeneId <- args$genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	284 + myGenes <- getGenes(cuff, myGeneId)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	286 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	287 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	288 + MDSplot(genes(cuff),replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	289 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	290 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	292 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	293 + else if (args$plotType == 'maplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	295 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	296 + else if (args$plotType == 'genetrack') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	297 + myGene <- getGene(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	298 + plotTracks(makeGeneRegionTrack(myGene))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	299 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	300 + },error = function(e) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	301 + write(paste("Failed:", e, sep=" "), stderr())
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	302 + q("no", 1, TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	303 + })
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	304 Fontconfig error: Cannot load default config file
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	305 Warning message:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	306 Removed 52 rows containing missing values (geom_point).
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	307 > devname = dev.off()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	308 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	309 > #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	310 >

Mercurial > repos > devteam > cummerbund

annotate test-data/maplot.txt @ 4:ba8fde59843d draft