fixed images and citations

topics/microbiome/tutorials/visualisation-ampvis/tutorial.md

@@ -27,14 +27,14 @@ 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.{% raw %} `{% cite Andersen2018 %}`{% endraw %}
+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 
-{% raw %} `{% cite ampvis-intro %}`{% endraw %}
-![overview of visualisation methods](../../images/overview.png 
+`{% 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 
 needs an OTU table and accepts the following formats for it: phyloseq, biom, 
@@ -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. {% raw %} `{% cite Andersen2018 %}`{% endraw %}
+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.
@@ -90,14 +90,6 @@ aggregate the OTUs.
 You can find the workflow "ampvis2 heatmap v3.0 (no group)" on Galaxy and use it for the tutorial.
 Metadata we used for this subset: metadata variable = Plant and metadata values = Aalborg East & Aalborg West.
 
-## Get data
-
-> <hands-on-title> Data upload and run a workflow </hands-on-title>
->
-> 1. Create a new history for this tutorial
-> 2. If not using your own data, import the files from [Zenodo]({{ page.zenodo_link }}) or from
-
-
 ## Get data
 
 > <hands-on-title> Data Upload </hands-on-title>
@@ -136,7 +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, 
+![Running the workflow](./images/heatmap_no_group.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.
@@ -146,7 +138,7 @@ 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/choose_parameters.png "Result of the heatmap")
 {: .details}
 
 > <details-title> metadata values error while running workflow </details-title>
@@ -187,11 +179,11 @@ We used 2 different metadata subsets:
 >
 > Result of the first metadata subset heatmap created with grouped by Plant data.
 > 
->![Result of the heatmap](../../images/heatmap_gr_by_plant.png "Result of the heatmap created with grouped by _Plant_")
+>![Result of the heatmap](./images/heatmap_gr_by_plant.png "Result of the heatmap created with grouped by _Plant_")
 > 
 > Result of the second metadata subset heatmap created with grouped by Year data.
 > 
->![Result of the heatmap](../../images/heatmap_gr_by_year.png "Result of the heatmap created with grouped by _Year_")
+>![Result of the heatmap](./images/heatmap_gr_by_year.png "Result of the heatmap created with grouped by _Year_")
 {: .details}
 
 ### heatmap (grouped with facets)
@@ -221,19 +213,19 @@ 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 
+>![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 
+>![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. {% raw %} `{% cite Andersen2018 %}`{% endraw %}
+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.
@@ -251,7 +243,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values
 >
 > Result of the ordination plot created with the method PCA.
 > 
->![Result of the ordiantion plot](../../images/ordination_pca.png "Result of the ordination plot created with the method PCA")
+>![Result of the ordiantion plot](./images/ordination_pca.png "Result of the ordination plot created with the method PCA")
 {: .details}
 
 ### ordination method: PCA plus trajectory: _date_
@@ -267,7 +259,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values
 >
 > Result of the ordination plot created with the method PCA plus using the trajectory date.
 > 
->![Result of the ordiantion plot](../../images/ordination_pca_date.png "Result of the ordination plot created with the method PCA plus using the trajectory date")
+>![Result of the ordiantion plot](./images/ordination_pca_date.png "Result of the ordination plot created with the method PCA plus using the trajectory date")
 {: .details}
 
 ### ordination method: CCA
@@ -283,12 +275,12 @@ Metadata we used for this subset: metadata variable = Plant and metadata values
 >
 > Result of the ordination plot created with the method CCA and the Hellinger transformation.
 > 
->![Result of the ordiantion plot](../../images/ordination_cca_hellinger.png "Result of the ordination plot created with the method CCA and the Hellinger transformation")
+>![Result of the ordiantion plot](./images/ordination_cca_hellinger.png "Result of the ordination plot created with the method CCA and the Hellinger transformation")
 {: .details}
 
 ## 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. {% raw %} `{% cite Andersen2018 %}`{% endraw %}
+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.
@@ -302,7 +294,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values
 >
 > Result of the boxplot grouped by Period.
 > 
->![Result of the boxplot](../../images/boxplot_period.png "Result of the boxplot grouped by Period")
+>![Result of the boxplot](./images/boxplot_period.png "Result of the boxplot grouped by Period")
 {: .details}
 
 > <tip-title>create a different boxplot</tip-title>
@@ -313,7 +305,7 @@ Metadata we used for this subset: metadata variable = Plant and metadata values
 > >
 > > Result of this boxplot.
 > >
-> > ![Result of the boxplot](../../images/boxplot_other.png "Result of this boxplot")
+> > ![Result of the boxplot](./images/boxplot_other.png "Result of this boxplot")
 > {: .details}
 {: .tip}
 
@@ -337,7 +329,7 @@ it. And as Number of taxa to show becomes a bit messy (for this data set at leas
 >
 > Result of the time series plot.
 > 
->![Result of the time series plot](../../images/timeseries.png "Result of the time series plot")
+>![Result of the time series plot](./images/timeseries.png "Result of the time series plot")
 {: .details}