diff --git a/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md b/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md index e7cf148f360666..3722cfc2bc917f 100644 --- a/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md +++ b/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md @@ -27,13 +27,13 @@ contributors: Microbiome analysis using amplicon sequencing is central to many ecological studies. The produced amplicon sequencing data are converted to OTU tables and represent the input -for the ampvis2 tool, where it can be visualised in various ways.`{% cite Andersen2018 %}` +for the ampvis2 tool, where it can be visualised in various ways.{% cite Andersen2018 %} If you already have amplicon data produced and ready to feed in and visualise it, then you can start with this tutorial. First of all you can put your data into a rarefraction curve to explore reads against number of OTUs. Than you can input your data into subsets and finaly create a heatmap, or a boxplot, or an ordination plot or even a timeseries plot out of it. Most of them are described in -`{% cite ampvis-intro %}` +{% cite ampvis-intro %} ![overview of visualisation methods](./images/overview.png "Overview of posible visualisation methods (taken from: Introduction to ampvis2 by Kasper Skytte Andersen)") Your data need to be in an acceptable format for the ampvis_load tool. The tool @@ -81,7 +81,7 @@ To create a heatmap, or ordination plot, or boxplot we now use normalised data. ## heatmaps We now can use our data, put them in subsets and create ungrouped, or grouped output or even grouped with facets. -The subsets are based on variable we set and available in the metadata. `{% cite Andersen2018 %}` +The subsets are based on variable we set and available in the metadata. {% cite Andersen2018 %} Note: in the next sections, we give you prepared workflows on Galaxy and the set of parameters to choose for running the indicated workflow. But some parameters are pre-chosen for you e.g. taxonomic level to aggregate the OTUs. @@ -128,8 +128,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values > {: .hands_on} -![Running the workflow](./images/heatmap_no_group.png "Running the workflow, -choose the right datasets and mandatory parameters") +![Running the workflow](./images/choose_parameters.png "Running the workflow, choose the right datasets and mandatory parameters") Choose the metadata variable as Plant and metadata values as Aalborg East & Aalborg West. In the next box you can see the resulting heatmap. @@ -138,7 +137,7 @@ In the next box you can see the resulting heatmap. > > Result of the heatmap created with ungrouped data. > ->![Result of the heatmap](./images/choose_parameters.png "Result of the heatmap") +>![Result of the heatmap](./images/heatmap_no_group.png "Result of the heatmap") {: .details} > metadata values error while running workflow @@ -156,9 +155,9 @@ In the next box you can see the resulting heatmap. ### heatmap (grouped) You can find the workflow "ampvis2 heatmap v2.0 (only group)" on Galaxy and use it for the tutorial. We used 2 different metadata subsets: -1) metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West. +1) metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West plus grouped by = Plant -2) metadata we used for this subset: metadata variable = Period and metadata values = Winter & Summer. +2) metadata we used for this subset: metadata variable = Period and metadata values = Winter & Summer plus grouped by = Year > Run a workflow @@ -189,9 +188,9 @@ We used 2 different metadata subsets: ### heatmap (grouped with facets) You can find the workflow "ampvis2 heatmap v1.0 (group+facet)" on Galaxy and use it for the tutorial. We used 2 different metadata subsets: -1) metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West. +1) metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West plus grouped by = Plant and facet by Period -2) metadata we used for this subset: metadata variable = Period and metadata values = Winter & Summer. +2) metadata we used for this subset: metadata variable = Period and metadata values = Winter & Summer plus grouped by = Year and facet by Period @@ -213,19 +212,17 @@ We used 2 different metadata subsets: > > Result of the first metadata subset heatmap created with grouped by Plant data and facet by Period. > ->![Result of the heatmap](./images/heatmap_plant_period.png "Result of the heatmap created with -> grouped by _Plant_ and facet by _Period_") +>![Result of the heatmap](./images/heatmap_plant_period.png "Result of the heatmap created with grouped by _Plant_ and facet by _Period_") > > Result of the second metadata subset heatmap created with grouped by Year data. > ->![Result of the heatmap](./images/heatmap_year_period.png "Result of the heatmap created with -> grouped by _Year_ and facet by _Period_") +>![Result of the heatmap](./images/heatmap_year_period.png "Result of the heatmap created with grouped by _Year_ and facet by _Period_") > {: .details} ## ordination plots We now can use our data, put them in subsets and create different plots by using different ordination methods. -Like with heatmaps, the subsets are based on variable we set and available in the metadata.`{% cite Andersen2018 %}` +Like with heatmaps, the subsets are based on variable we set and available in the metadata.{% cite Andersen2018 %} Note: in the next sections, we give you prepared workflows on Galaxy and the set of parameters to choose for running the indicated workflow. But some parameters are pre-chosen for you e.g. ordination method, transformation (if used) and others like to colour and label the points or frames. @@ -280,7 +277,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values ## boxplot We now can use our data, put them in subsets and create a boxplot. -Like with heatmaps, the subsets are based on variable we set and available in the metadata. `{% cite Andersen2018 %}` +Like with heatmaps, the subsets are based on variable we set and available in the metadata. {% cite Andersen2018 %} Note: in the prepared workflow on Galaxy we provide in this tutorial some parameters are pre-chosen for you e.g. number of taxa to show. The samples are grouped by _Period_. Metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West.