Hello . SO...after using your suggestions for looking into uwunifrac$data$Vectors, I discovered that the sample IDs had to be in the format of SampleID. Furthermore, I also figured out for "shannon" I was selecting a dataset and NOT a variable. It was supposed to be "shannons". So what the majority of it was was simple tab-completing errors and the stinking letter "S" haha. The code below worked beautifully and I was even able to manipulate the graphic further. Thank you so much for your help!!!
metadata <- readr::read_tsv('/Users/SamuraiSteve/Dropbox/gfic_data_analysis/qiime2/03_metadata/metadata_all-samples.txt')
uwunifrac <- read_qza('/Users/SamuraiSteve/Dropbox/gfic_data_analysis/qiime2/unweighted_unifrac_pcoa_results.qza')
shannon <- read_qza('/Users/SamuraiSteve/Dropbox/gfic_data_analysis/qiime2/shannon_vector.qza')$data %>% rownames_to_column('SampleID')
uwunifrac$data$Vectors %>%
select(SampleID, PC1, PC2) %>%
left_join(metadata) %>%
left_join(shannon) %>%
filter(room_function != '01_animal-swab',
room_function != '01_environment',
room_function != '01_hand-swab') %>%
mutate(sample_site = gsub('door', 'Door', sample_site),
sample_site = gsub('drain', 'Drain', sample_site),
room_function = gsub('00_', '', room_function),
room_function = gsub('02_', '', room_function),
room_function = gsub('03_', '', room_function),
room_function = gsub('04_', '', room_function),
room_function = gsub('05_', '', room_function),
room_function = fct_relevel(room_function, 'live animal', 'harvest',
'fabrication and processing',
'product holding'),
room_function = fct_recode(room_function,
'fabrication &\nprocessing' = 'fabrication and processing'),
room_function = fct_recode(room_function, 'product \nholding' = 'product holding'),
listeria_present = as.factor(listeria_present),
listeria_present = fct_relevel(listeria_present, 'yes', 'no')) -> data
prism <- carto_pal(12, 'Prism')
prism <- c("#5F4690", "#38A6A5", "#0F8554", "#CC503E", "#94346E","#994E95")
data %>% ggplot(aes(x = PC1, y = PC2, color=room_function, shape=listeria_present, size = shannons)) +
geom_point(alpha=0.3) +
guides(color = guide_legend(override.aes = list(size = 4))) +
guides(shape = guide_legend(override.aes = list(size = 4))) +
theme_few() +
theme(axis.text.x = element_text(angle = 45, vjust = 0.99, hjust = 0.95),
legend.spacing.x = unit(0.1, 'cm'),
legend.spacing.y = unit(0.1, 'cm'),
text = element_text(family = "Times New Roman",
size = 16)) +
scale_shape_manual(values=c(16,1), name="Listeria Presence") +
scale_size_continuous(name="Shannon Diversity") +
scale_color_manual(values = prism, name="Room Function")