SW_AmpIllumina-B: vis readme update

 * Add output prefix to output file names

Author: torres-alexis

Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/workflow_code/visualizations/README.md

@@ -84,16 +84,16 @@ Additionally, the `RColorBrewer_Palette` variable can be modified in the script.
 * taxonomy_GLAmpSeq.tsv (output from [GL-DPPD-7104-B step 5g](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md#5g-generating-and-writing-standard-outputs))
 
 **Output Data:**
-* **dendrogram_by_group{assay_suffix}.png** (dendrogram of euclidean distance - based hierarchical clustering of the samples, colored by experimental groups)
-* **rarefaction_curves{assay_suffix}.png** (Rarefaction curves plot for all samples)
-* **richness_and_diversity_estimates_by_sample{assay_suffix}.png** (Richness and diversity estimates plot for all samples)
-* **richness_and_diversity_estimates_by_group{assay_suffix}.png** (Richness and diversity estimates plot for all groups)
-* **relative_phyla{assay_suffix}.png** (taxonomic summaries plot based on phyla, for all samples)
-* **relative_classes{assay_suffix}.png** (taxonomic summaries plot based on class, for all samples)
-* **samplewise_phyla{assay_suffix}.png** (taxonomic summaries plot based on phyla, for all samples)
-* **samplewise_classes{assay_suffix}.png** (taxonomic summaries plot based on class, for all samples)
-* **PCoA_w_labels{assay_suffix}.png** (principle Coordinates Analysis plot of VST transformed ASV counts, with sample labels)
-* **PCoA_without_labels{assay_suffix}.png** (principle Coordinates Analysis plot of VST transformed ASV counts, without sample labels)
-* **normalized_counts{assay_suffix}.tsv** (size factor normalized ASV counts table)
-* **group1_vs_group2.csv** (differential abundance tables for all pairwise contrasts of groups)
-* **volcano_group1_vs_group2.png** (volcano plots for all pairwise contrasts of groups)
+* **{output_prefix}dendrogram_by_group{assay_suffix}.png** (dendrogram of euclidean distance - based hierarchical clustering of the samples, colored by experimental groups)
+* **{output_prefix}rarefaction_curves{assay_suffix}.png** (Rarefaction curves plot for all samples)
+* **{output_prefix}richness_and_diversity_estimates_by_sample{assay_suffix}.png** (Richness and diversity estimates plot for all samples)
+* **{output_prefix}richness_and_diversity_estimates_by_group{assay_suffix}.png** (Richness and diversity estimates plot for all groups)
+* **{output_prefix}relative_phyla{assay_suffix}.png** (taxonomic summaries plot based on phyla, for all samples)
+* **{output_prefix}relative_classes{assay_suffix}.png** (taxonomic summaries plot based on class, for all samples)
+* **{output_prefix}samplewise_phyla{assay_suffix}.png** (taxonomic summaries plot based on phyla, for all samples)
+* **{output_prefix}samplewise_classes{assay_suffix}.png** (taxonomic summaries plot based on class, for all samples)
+* **{output_prefix}PCoA_w_labels{assay_suffix}.png** (principle Coordinates Analysis plot of VST transformed ASV counts, with sample labels)
+* **{output_prefix}PCoA_without_labels{assay_suffix}.png** (principle Coordinates Analysis plot of VST transformed ASV counts, without sample labels)
+* **{output_prefix}normalized_counts{assay_suffix}.tsv** (size factor normalized ASV counts table)
+* **{output_prefix}group1_vs_group2.csv** (differential abundance tables for all pairwise contrasts of groups)
+* **{output_prefix}volcano_group1_vs_group2.png** (volcano plots for all pairwise contrasts of groups)