Mercurial > repos > proteore > proteore_goprofiles
annotate goprofiles.R @ 5:781072a65600 draft
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
author | proteore |
---|---|
date | Wed, 19 Sep 2018 05:49:06 -0400 |
parents | 715002a394ec |
children | 6afe8166a9a4 |
rev | line source |
---|---|
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
1 # Load necessary libraries |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
2 library(goProfiles,quietly = TRUE) |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
3 |
4
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
4 # Read file and return file content as data.frame |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
5 readfile = function(filename, header) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
6 if (header == "true") { |
4
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
7 # Read only first line of the file as header: |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
8 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
9 #Read the data of the files (skipping the first row) |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
10 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
11 # Remove empty rows |
4
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
12 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
13 #And assign the header to the data |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
14 names(file) <- headers |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
15 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
16 else { |
4
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
17 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "") |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
18 # Remove empty rows |
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
19 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
20 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
21 return(file) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
22 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
23 |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
24 check_ids <- function(vector,type) { |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
25 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$" |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
26 entrez_id = "^'[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$" |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
27 if (type == "Entrez"){ |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
28 return(grepl(entrez_id,vector)) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
29 } else if (type == "UniProt") { |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
30 return(grepl(uniprot_pattern,vector)) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
31 } |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
32 } |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
33 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
34 getprofile = function(ids, id_type, level, duplicate,species) { |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
35 #################################################################### |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
36 # Arguments |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
37 # - ids: list of input IDs |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
38 # - id_type: type of input IDs (UniProt/ENTREZID) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
39 # - level |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
40 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE) |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
41 # - species |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
42 #################################################################### |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
43 |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
44 library(species, character.only = TRUE, quietly = TRUE) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
45 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
46 if (species=="org.Hs.eg.db"){ |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
47 package=org.Hs.eg.db |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
48 } else if (species=="org.Mm.eg.db"){ |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
49 package=org.Mm.eg.db |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
50 } |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
51 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
52 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
53 |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
54 # Check if level is number |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
55 if (! as.numeric(level) %% 1 == 0) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
56 stop("Please enter an integer for level") |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
57 } else { |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
58 level = as.numeric(level) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
59 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
60 #genes = as.vector(file[,ncol]) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
61 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
62 # Extract Gene Entrez ID |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
63 if (id_type == "Entrez") { |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
64 id = select(package, ids, "ENTREZID", multiVals = "first") |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
65 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))] |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
66 } else { |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
67 genes_ids = c() |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
68 id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first") |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
69 if (duplicate == "TRUE") { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
70 id = unique(id) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
71 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
72 print(id[[1]]) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
73 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))] |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
74 # IDs that have NA ENTREZID |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
75 NAs = id$UNIPROT[which(is.na(id$ENTREZID))] |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
76 print("IDs unable to convert to ENTREZID: ") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
77 print(NAs) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
78 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
79 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
80 # Create basic profiles |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
81 profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
82 profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
83 profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
84 profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
85 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
86 # Print profile |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
87 # printProfiles(profile) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
88 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
89 return(c(profile.CC, profile.MF, profile.BP, profile.ALL)) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
90 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
91 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
92 # Plot profiles to PNG |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
93 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
94 if (!is.null(profile.CC)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
95 png("profile.CC.png") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
96 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
97 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
98 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
99 if (!is.null(profile.BP)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
100 png("profile.BP.png") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
101 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
102 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
103 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
104 if (!is.null(profile.MF)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
105 png("profile.MF.png") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
106 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
107 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
108 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
109 if (!is.null(profile.ALL)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
110 png("profile.ALL.png") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
111 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
112 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
113 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
114 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
115 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
116 # Plot profiles to JPEG |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
117 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
118 if (!is.null(profile.CC)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
119 jpeg("profile.CC.jpeg") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
120 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
121 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
122 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
123 if (!is.null(profile.BP)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
124 jpeg("profile.BP.jpeg") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
125 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
126 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
127 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
128 if (!is.null(profile.MF)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
129 jpeg("profile.MF.jpeg") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
130 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
131 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
132 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
133 if (!is.null(profile.ALL)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
134 jpeg("profile.ALL.jpeg") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
135 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
136 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
137 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
138 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
139 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
140 # Plot profiles to PDF |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
141 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
142 if (!is.null(profile.CC)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
143 pdf("profile.CC.pdf") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
144 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
145 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
146 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
147 if (!is.null(profile.BP)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
148 pdf("profile.BP.pdf") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
149 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
150 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
151 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
152 if (!is.null(profile.MF)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
153 pdf("profile.MF.pdf") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
154 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
155 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
156 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
157 if (!is.null(profile.ALL)) { |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
158 #print("all") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
159 pdf("profile.ALL.pdf") |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
160 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title) |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
161 dev.off() |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
162 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
163 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
164 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
165 goprofiles = function() { |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
166 args <- commandArgs(TRUE) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
167 if(length(args)<1) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
168 args <- c("--help") |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
169 } |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
170 |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
171 # Help section |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
172 if("--help" %in% args) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
173 cat("Selection and Annotation HPA |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
174 Arguments: |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
175 --input_type: type of input (list of id or filename) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
176 --input: input |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
177 --ncol: the column number which you would like to apply... |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
178 --header: true/false if your file contains a header |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
179 --id_type: the type of input IDs (UniProt/EntrezID) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
180 --onto_opt: ontology options |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
181 --plot_opt: plot extension options (PDF/JPEG/PNG) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
182 --level: 1-3 |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
183 --per |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
184 --title: title of the plot |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
185 --duplicate: remove dupliate input IDs (true/false) |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
186 --text_output: text output filename \n |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
187 --species") |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
188 q(save="no") |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
189 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
190 |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
191 # Parse arguments |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
192 parseArgs <- function(x) strsplit(sub("^--", "", x), "=") |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
193 argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
194 args <- as.list(as.character(argsDF$V2)) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
195 names(args) <- argsDF$V1 |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
196 |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
197 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda") |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
198 #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda") |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
199 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
200 id_type = args$id_type |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
201 input_type = args$input_type |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
202 if (input_type == "text") { |
4
715002a394ec
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
proteore
parents:
2
diff
changeset
|
203 input = strsplit(args$input, "[ \t\n]+")[[1]] |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
204 } else if (input_type == "file") { |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
205 filename = args$input |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
206 ncol = args$ncol |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
207 # Check ncol |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
208 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
209 stop("Please enter an integer for level") |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
210 } else { |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
211 ncol = as.numeric(gsub("c", "", ncol)) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
212 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
213 header = args$header |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
214 # Get file content |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
215 file = readfile(filename, header) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
216 # Extract Protein IDs list |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
217 input = c() |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
218 for (row in as.character(file[,ncol])) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
219 input = c(input, strsplit(row, ";")[[1]][1]) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
220 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
221 } |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
222 |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
223 if (! any(check_ids(input,id_type))){ |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
224 stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file")) |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
225 } |
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
226 |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
227 ontoopt = strsplit(args$onto_opt, ",")[[1]] |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
228 #print(ontoopt) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
229 #plotopt = strsplit(args[3], ",") |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
230 plotopt = args$plot_opt |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
231 level = args$level |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
232 per = as.logical(args$per) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
233 title = args$title |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
234 duplicate = args$duplicate |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
235 text_output = args$text_output |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
236 species=args$species |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
237 |
5
781072a65600
planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty
proteore
parents:
4
diff
changeset
|
238 profiles = getprofile(input, id_type, level, duplicate,species) |
1
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
239 profile.CC = profiles[1] |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
240 #print(profile.CC) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
241 profile.MF = profiles[2] |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
242 #print(profile.MF) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
243 profile.BP = profiles[3] |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
244 #print(profile.BP) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
245 profile.ALL = profiles[-3:-1] |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
246 #print(profile.ALL) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
247 #c(profile.ALL, profile.CC, profile.MF, profile.BP) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
248 |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
249 if ("CC" %in% ontoopt) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
250 write.table(profile.CC, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
251 if (grepl("PNG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
252 plotPNG(profile.CC=profile.CC, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
253 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
254 if (grepl("JPEG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
255 plotJPEG(profile.CC = profile.CC, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
256 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
257 if (grepl("PDF", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
258 plotPDF(profile.CC = profile.CC, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
259 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
260 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
261 if ("MF" %in% ontoopt) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
262 write.table(profile.MF, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
263 if (grepl("PNG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
264 plotPNG(profile.MF = profile.MF, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
265 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
266 if (grepl("JPEG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
267 plotJPEG(profile.MF = profile.MF, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
268 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
269 if (grepl("PDF", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
270 plotPDF(profile.MF = profile.MF, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
271 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
272 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
273 if ("BP" %in% ontoopt) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
274 write.table(profile.BP, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
275 if (grepl("PNG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
276 plotPNG(profile.BP = profile.BP, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
277 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
278 if (grepl("JPEG", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
279 plotJPEG(profile.BP = profile.BP, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
280 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
281 if (grepl("PDF", plotopt)) { |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
282 plotPDF(profile.BP = profile.BP, per=per, title=title) |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
283 } |
1236ee08ccb8
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
284 } |
0
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
285 } |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
286 |
d89c09253c8d
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
287 goprofiles() |