Visualize take 2

[sr320]

Share a visualization that clearly shows the outcome of your analyses. For example - what is differently expressed, or abundance of taxa..

[jdduprey]

I mostly want to visualize benthic community diversity across time and location, but in order to do that I need to decide on my benthic functional groups, which is more challenging than I anticipated with ~500 taxa (and my limited algae knowledge).

I've been doing some data exploration looking at relative abundance in addition to community structure. Here are some of my data exploration figures so far, including nReads plotted against environmental conditions, and some low resolution time series.

March looks like a good month for periwinkles.

[skreling]

Here are some of my visualizations I've made.

Because there are SO many taxa in the dataset, I've limited a lot of the visualizations to taxa representing ≥ 1% of reads, and grouping the lower percentages in an 'other' category which represents ~30% of the data which is a lot, so I'm not really sure what to do with that.

https://github.com/fish546-2021/Sam-Metabarcoding/blob/main/Results/Bat/S2_Cleaned_Barplot_over1percent.pdf https://github.com/fish546-2021/Sam-Metabarcoding/blob/main/Results/Bat/S2_piechart_greaterother.pdf

Here are also some I created for the mouse dataset, which was nice because this dataset reference database also had higher taxonomy that I could easily pull into figures https://github.com/fish546-2021/Sam-Metabarcoding/blob/main/Results/Mouse/Microbiome_Tree https://github.com/fish546-2021/Sam-Metabarcoding/blob/main/Results/Mouse/mouse_bargraph

[aspencoyle]

Here are some visualizations! Each image is a pairwise comparison between groups of infected crab. Amb/elev/low correspond to temperature treatment, 0/2/17 correspond to days since the temperature treatments began. For instance, elev2_vs_amb02 means libraries from elevated-temperature group crab on Day 2 vs. libraries from ambient-temperature group crab on Days 0 and 2.

The visualization shows differentially-enriched biological processes, as determined by gene ontology terms. Visualizations were created using the R package GO-MWU

[jdduprey]

@afcoyle these are cool, is there a name for the branching biological process diagrams?

[aspencoyle]

Thanks @jdduprey! It's a hierarchical clustering tree, which the package I used for analysis - GO-MWU created automatically as part of its output!

[meganewing]

heatmap volcano

now if only I can figure out how to interpret them...

[laurel-nave-powers]

I won't be able to have SNPs by the end of the day, so here is some intermediate visualization in the form of fastqc. file:///Users/laurelnave-powers/Desktop/GitHub/Laurel-genes/analyses/fastqc/HIPPLAT_NEF95054_S2_R1_fastqc.html file:///Users/laurelnave-powers/Desktop/GitHub/Laurel-genes/analyses/fastqc/HIPPLAT_NEF95054_S2_R2_fastqc.html file:///Users/laurelnave-powers/Desktop/GitHub/Laurel-genes/analyses/fastqc/MICPACI_UW157426_S7_R1_fastqc.html file:///Users/laurelnave-powers/Desktop/GitHub/Laurel-genes/analyses/fastqc/MICPACI_UW157426_S7_R2_fastqc.html

[Brybrio]

https://github.com/fish546-2021/Bryan-Eelgrass/blob/main/Figs/Pop_assignment.png