diff --git a/frontend/src/main/java/de/thm/spring/controller/ApplicationController.java b/frontend/src/main/java/de/thm/spring/controller/ApplicationController.java index f905c4440be8c4f787b7673aae3e69e0ac7d1fd2..1a86efbbcba137dfca546daaee71ca5b8779d665 100644 --- a/frontend/src/main/java/de/thm/spring/controller/ApplicationController.java +++ b/frontend/src/main/java/de/thm/spring/controller/ApplicationController.java @@ -117,6 +117,12 @@ public class ApplicationController implements ErrorController { return "faq"; } + + @RequestMapping("/tutorial") + public String tutorial() { + + return "tutorial"; + } @RequestMapping("/contact") public String contact(){ diff --git a/frontend/src/main/java/de/thm/spring/controller/SampleController.java b/frontend/src/main/java/de/thm/spring/controller/SampleController.java index 56a05e43057407f5f4ffc9cc5a6c32d1baf6d2ef..0bcd270e1e5a48b0d33f128c226b6ea4ff67238d 100644 --- a/frontend/src/main/java/de/thm/spring/controller/SampleController.java +++ b/frontend/src/main/java/de/thm/spring/controller/SampleController.java @@ -50,10 +50,10 @@ public class SampleController { if(System.getenv("HOME").contains("menzel")) { String path = "/home/menzel/Desktop/THM/lfba/enhort"; - samplefilepath = path+"/HIV-hg19.bed"; + samplefilepath = path + "/sites.hiv.all.wu_03.tab"; } else { String path = "/home/mmnz21/enhort"; - samplefilepath = path+"/HIV-hg19.bed"; + samplefilepath = path + "/sites.hiv.all.wu_03.tab"; } if (!new File(samplefilepath).exists()) { @@ -72,7 +72,7 @@ public class SampleController { currentSession.setOriginalFilename("HIV"); BackendCommand backendCommand = //new BackendCommand(userSites, Command.Task.ANALZYE_SINGLE); - new BackendCommand.Builder(Command.Task.ANALZYE_SINGLE, userSites.getAssembly()).sites(userSites).build(); + new BackendCommand.Builder(Command.Task.ANALZYE_SINGLE, userSites.getAssembly()).sites(userSites).minBg(userSites.getPositionCount()).build(); try { /////////// Run analysis //////////// diff --git a/frontend/src/main/resources/static/css/faq.css b/frontend/src/main/resources/static/css/faq.css index f85cfdfcd7855e527388715d481b434cd867892f..51bd1f14b0c3418f942872a3e81b62e3d3cf1a9e 100644 --- a/frontend/src/main/resources/static/css/faq.css +++ b/frontend/src/main/resources/static/css/faq.css @@ -18,3 +18,10 @@ p { #faqlogo { width: inherit; } + +.tutorialimage { + width: 700px; + border: 1px solid black; + margin-top: 30px; + margin-bottom: 30px; +} \ No newline at end of file diff --git a/frontend/src/main/resources/static/img/tutorial/tut1.png b/frontend/src/main/resources/static/img/tutorial/tut1.png new file mode 100644 index 0000000000000000000000000000000000000000..b7bfdec8540041eb194fad4acb9fab51463ac4e6 Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut1.png differ diff --git a/frontend/src/main/resources/static/img/tutorial/tut2.png b/frontend/src/main/resources/static/img/tutorial/tut2.png new file mode 100644 index 0000000000000000000000000000000000000000..95265e83631ce0f2a6d290a9ed927fa9f7537b65 Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut2.png differ diff --git a/frontend/src/main/resources/static/img/tutorial/tut3.png b/frontend/src/main/resources/static/img/tutorial/tut3.png new file mode 100644 index 0000000000000000000000000000000000000000..a11de178e522bb542adb0a710c03b7a47b3988a6 Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut3.png differ diff --git a/frontend/src/main/resources/static/img/tutorial/tut4.png b/frontend/src/main/resources/static/img/tutorial/tut4.png new file mode 100644 index 0000000000000000000000000000000000000000..2d0c0f911cde99b88cfb418287f355d93467d880 Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut4.png differ diff --git a/frontend/src/main/resources/static/img/tutorial/tut5.png b/frontend/src/main/resources/static/img/tutorial/tut5.png new file mode 100644 index 0000000000000000000000000000000000000000..3eddba25846633cc6fc4926cac07ec6a07002583 Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut5.png differ diff --git a/frontend/src/main/resources/static/img/tutorial/tut6.png b/frontend/src/main/resources/static/img/tutorial/tut6.png new file mode 100644 index 0000000000000000000000000000000000000000..d52dfe47f5e59c2947e9595bc41e8e56cb50abad Binary files /dev/null and b/frontend/src/main/resources/static/img/tutorial/tut6.png differ diff --git a/frontend/src/main/resources/templates/faq.html b/frontend/src/main/resources/templates/faq.html index 53da3310080c63e8fb1d692e4fdfb50516b3abb3..806476019ced57bd27a96057a0fce94f582f4db1 100644 --- a/frontend/src/main/resources/templates/faq.html +++ b/frontend/src/main/resources/templates/faq.html @@ -34,8 +34,7 @@ Analysis. Enhort then tests your genomic positions against a set of annotations. Using the Guided Analysis you can select annotations, based on your assembly number and cellline, see the section about the Guided Analysis usage below on this page. The quickstart upload uses a curated - list of annotations, containing genes and gene related features, genotoxicity, accessibility and a - selection of histone modifications. + list of annotations, containing genes and gene related features to test your sites against.

@@ -52,7 +51,8 @@

- If you are interested in seeing some results use the sample data link. + If you are interested in seeing some results use the sample data link. A more + comprehensive tutorial is available here.

Guided Analysis

diff --git a/frontend/src/main/resources/templates/tutorial.html b/frontend/src/main/resources/templates/tutorial.html new file mode 100644 index 0000000000000000000000000000000000000000..4eb608b6e072c07eec97b82a9bee80a34a9468be --- /dev/null +++ b/frontend/src/main/resources/templates/tutorial.html @@ -0,0 +1,117 @@ + + + + + Enhort - Genomic Position Profiling - Tutorial + + + + + + + + + + + + + +
+ +
+
+ + + +

Tutorial

+ +

+ In this short tutorial a set of 1141475 HIV integration sites are analysed using Enhort. + +

+

Upload integration sites

+
+ +

+ At first, integration sites have to uploaded in a .bed-file. In this example set of about 1m HIV integration + sites taken from the + Retrovirus Integration Database is used. The wizard is selected on + the main page: + +

+ + + +

+ And on the following page the .bed-file is selected on the local computer. + +

+

Select annotations

+
+ + + The sites are then uploaded and the overview for available annotations is shown: + + + +

+ Single annotations can be selected by clicking on the blue squares. A set of annotations for a cell line or + all annotations in a column + can be selected by clicking on the row or column header. For example, all cell line independent annotations + are selected in the following example, as well as + annotations for HeLa: + +

+ + + +

Review results and add a covariate

+
+ +

+ The results for the given sites and selected covariates are then displayed in a table, containing the effect + size and p value of each annotation, as well + as overview over the annotation groups. Each row can be expanded to get exact integration counts for each + annotation: + +

+ + +

+ + From here the user can select covariates to alter the integation preference + of the background control sites. For example, HIV is known to integrate near genes which is observable in + the upper image. The annotation track RefSeq genes can + be selected as covariate to adapt the background for this known preference. To do this the marked checkbox + is selected and with the button 'Run again' the + background is changed. In the following image we see RefSeq genes was added to list of covariate on the + right and now has the exact same integration preference as the HIV sites: + +

+ + +

+ + This adaptation then changes the significance and fold change of several annotations tracks in the main + table. In the following the complete table of selected annotations is shown + with 'houskeeping genes' expanded to show exact integration counts: +

+ + + + +

Further possibilites

+
+ +

+ In the upper part different tabs are located containing further analysis of the given sites, as well as the + option to download the background sites or results. + Depending on the individual scientific question other covariates can be selected to build a specialized + background model. +

+ +
+
+ + \ No newline at end of file