Mercurial > repos > proteore > proteore_goprofiles
changeset 9:948fecb6a40b draft
planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty
| author | proteore |
|---|---|
| date | Mon, 04 Mar 2019 05:48:48 -0500 |
| parents | 386145573c19 |
| children | 2138e0035e57 |
| files | goprofiles.R goprofiles.xml |
| diffstat | 2 files changed, 41 insertions(+), 13 deletions(-) [+] |
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--- a/goprofiles.R Tue Dec 18 09:54:57 2018 -0500 +++ b/goprofiles.R Mon Mar 04 05:48:48 2019 -0500 @@ -79,30 +79,42 @@ #print("IDs unable to convert to ENTREZID: ") #print(NAs) } - # Create basic profiles profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T) - # Print profile # printProfiles(profile) return(c(profile.CC, profile.MF, profile.BP, profile.ALL)) } +#return height and width of plot in inches from profile +plot_size_from_nb_onto <- function(profile){ + width=10 + range = seq(50, 2000, by=25) + names(range) = seq(8,242, by=3) + nb_onto = round(nrow(profile[[1]])/25)*25 + height= as.integer(names(which(range==nb_onto))) + return (c(width,height)) +} + make_plot <- function(profile,percent,title,onto,plot_opt){ + tmp <- plot_size_from_nb_onto (profile) + width <- tmp[1] + height <- tmp[2] + if (plot_opt == "PDF") { file_name=paste("profile_",onto,".pdf",collapse="",sep="") - pdf(file_name) + pdf(file_name, width=width, heigh=height) } else if (plot_opt == "JPEG"){ file_name=paste("profile_",onto,".jpeg",collapse="",sep="") - jpeg(file_name) + jpeg(file_name,width=width, height=height, units = "in", res=100) } else if (plot_opt == "PNG"){ file_name=paste("profile_",onto,".png",collapse="",sep="") - png(file_name) + png(file_name,width=width, height=height, units = "in", res=100) } plotProfiles(profile, percentage=percent, multiplePlots=FALSE, aTitle=title) dev.off() @@ -179,7 +191,7 @@ species=args$species profiles = getprofile(input, id_type, level, duplicate,species) - + for (index in onto_pos) { onto = names(profiles[index]) profile=profiles[index]
--- a/goprofiles.xml Tue Dec 18 09:54:57 2018 -0500 +++ b/goprofiles.xml Mon Mar 04 05:48:48 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2018.12.12"> +<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.02.27"> <description>(Human, Mouse) [goProfiles]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -8,6 +8,7 @@ <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> <requirement type="package" version="1.38.0">goprofiles</requirement> + </requirements> <stdio> <exit_code range="1:" /> @@ -59,7 +60,9 @@ </when> <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> - <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> <param name="id_type" type="select" label="Select type of IDs list" > <option value="Entrez">Entrez Gene ID</option> @@ -82,13 +85,26 @@ <option value="1">1</option> <option value="2" selected="True">2</option> <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> </param> <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" /> - <param type="text" name="title" label="Enter title of your figure" /> + <param type="text" name="title" label="Enter title of your figure"> + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping> + <add source=" " target=""/> + </mapping> + </sanitizer> + </param> <param type="select" name="plot_opt" label="Plot file format"> - <option value="PNG">png</option> + <option value="PNG" selected="True">png</option> <option value="JPEG">jpeg</option> - <option value="PDF" selected="True">pdf</option> + <option value="PDF">pdf</option> </param> </inputs> @@ -148,13 +164,13 @@ "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF) -"Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3). In general the higher the level, the more semantically specific the term is. +"Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is. ----- **Ouput** -Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category. +Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category. text output: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)