Mercurial > repos > mingchen0919 > rmarkdown_deseq2
annotate DESeq_results_render.R @ 6:2f8ddef8d545 draft
update deseq2
| author | mingchen0919 |
|---|---|
| date | Tue, 07 Nov 2017 13:50:32 -0500 |
| parents | 7231d7e8d3ed |
| children |
| rev | line source |
|---|---|
| 6 | 1 library(getopt) |
| 2 library(rmarkdown) | |
| 3 library(htmltools) | |
| 4 library(dplyr) | |
| 5 library(DESeq2) | |
| 6 library(pheatmap) | |
| 7 library(genefilter) | |
| 8 library(DT) | |
| 9 library(stringi) | |
| 10 library(RColorBrewer) | |
| 11 library(ggplot2) | |
|
0
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
12 |
| 6 | 13 ##============ Sink warnings and errors to a file ============== |
| 14 ## use the sink() function to wrap all code within it. | |
| 15 ##============================================================== | |
| 16 zz = file('warnings_and_errors.txt') | |
| 17 sink(zz) | |
| 18 sink(zz, type = 'message') | |
| 19 ##---------below is the code for rendering .Rmd templates----- | |
| 20 | |
| 21 ##=============STEP 1: handle command line arguments========== | |
| 22 ## | |
| 23 ##============================================================ | |
| 24 # column 1: the long flag name | |
| 25 # column 2: the short flag alias. A SINGLE character string | |
| 26 # column 3: argument mask | |
| 27 # 0: no argument | |
| 28 # 1: argument required | |
| 29 # 2: argument is optional | |
| 30 # column 4: date type to which the flag's argument shall be cast. | |
| 31 # possible values: logical, integer, double, complex, character. | |
| 32 #------------------------------------------------------------- | |
| 33 #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++ | |
| 34 # 1. short flag alias should match the flag in the command section in the XML file. | |
| 35 # 2. long flag name can be any legal R variable names | |
| 36 # 3. two names in args_list can have common string but one name should not be a part of another name. | |
| 37 # for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems. | |
| 38 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| 39 args_list=list() | |
| 40 ##------- 1. input data --------------------- | |
| 41 args_list$ECHO = c('echo', 'e', '1', 'character') | |
| 42 args_list$DESEQ_WORKSPACE = c('deseq_workspace', 'W', '1', 'character') | |
| 43 args_list$CONTRAST_FACTOR = c('contrast_factor', 'C', '1', 'character') | |
| 44 args_list$TREATMENT_LEVEL = c('treatment_level', 'T', '1', 'character') | |
| 45 args_list$CONDITION_LEVEL = c('condition_level', 'K', '1', 'character') | |
| 46 args_list$CLUSTERING_FACTORS = c('clustering_factors', 'M', '1', 'character') | |
| 47 ##--------2. output report and outputs -------------- | |
| 48 args_list$REPORT_HTML = c('report_html', 'r', '1', 'character') | |
| 49 args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character') | |
| 50 args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character') | |
| 51 args_list$DESEQ_RESULTS = c('deseq_results', 'R', '1', 'character') | |
| 52 ##--------3. .Rmd templates in the tool directory ---------- | |
| 53 args_list$deseq_results_RMD = c('deseq_results_rmd', 't', '1', 'character') | |
| 54 ##----------------------------------------------------------- | |
| 55 opt = getopt(t(as.data.frame(args_list))) | |
|
0
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
56 |
|
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
57 |
| 6 | 58 |
| 59 ##=======STEP 2: create report directory (optional)========== | |
| 60 ## | |
| 61 ##=========================================================== | |
| 62 dir.create(opt$report_dir) | |
| 63 | |
| 64 ##=STEP 3: replace placeholders in .Rmd with argument values= | |
| 65 ## | |
| 66 ##=========================================================== | |
| 67 #++ need to replace placeholders with args values one by one+ | |
| 68 readLines(opt$deseq_results_rmd) %>% | |
| 69 (function(x) { | |
| 70 gsub('ECHO', opt$echo, x) | |
| 71 }) %>% | |
| 72 (function(x) { | |
| 73 gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x) | |
| 74 }) %>% | |
| 75 (function(x) { | |
| 76 gsub('CONTRAST_FACTOR', opt$contrast_factor, x) | |
| 77 }) %>% | |
| 78 (function(x) { | |
| 79 gsub('TREATMENT_LEVEL', opt$treatment_level, x) | |
| 80 }) %>% | |
| 81 (function(x) { | |
| 82 gsub('CONDITION_LEVEL', opt$condition_level, x) | |
| 83 }) %>% | |
| 84 (function(x) { | |
| 85 gsub('CLUSTERING_FACTORS', opt$clustering_factors, x) | |
| 86 }) %>% | |
| 87 (function(x) { | |
| 88 gsub('REPORT_DIR', opt$report_dir, x) | |
| 89 }) %>% | |
| 90 (function(x) { | |
| 91 gsub('DESEQ_RESULTS', opt$deseq_results, x) | |
| 92 }) %>% | |
| 93 (function(x) { | |
| 94 fileConn = file('deseq_results.Rmd') | |
| 95 writeLines(x, con=fileConn) | |
| 96 close(fileConn) | |
| 97 }) | |
| 98 | |
|
0
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
99 |
| 6 | 100 ##=============STEP 4: render .Rmd templates================= |
| 101 ## | |
| 102 ##=========================================================== | |
| 103 render('deseq_results.Rmd', output_file = opt$report_html) | |
|
0
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
104 |
|
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff
changeset
|
105 |
| 6 | 106 ##--------end of code rendering .Rmd templates---------------- |
| 107 sink() | |
| 108 ##=========== End of sinking output============================= |