In sponslerdb/vsearchR:

Load vsearch output

CT pollen

trnL_CT <- load_blast6("~/vsearchr/inst/extdata/trnL_vsearch_CT.output/")
rbcL_CT <- load_blast6("~/vsearchr/inst/extdata/rbcL_vsearch_CT.output/")
ITS2_CT <- load_blast6("~/vsearchr/inst/extdata/ITS2_vsearch_CT.output/")

Load taxonomy tables

CT pollen

trnL_CT_tax <- load_MTXA("~/vsearchr/inst/extdata/trnL_CT_Amplicons2.tax")
rbcL_CT_tax <- load_MTXA("~/vsearchr/inst/extdata/rbcL_CT_Amplicons.tax")
ITS2_CT_tax <- load_MTXA("~/vsearchr/inst/extdata/ITS2_CT_Amplicons.tax")

Join vsearch output to taxonomy tables

CT pollen

trnL_CT_join <- tax_join(trnL_CT, trnL_CT_tax, min_id = 92.5)
rbcL_CT_join <- tax_join(rbcL_CT, rbcL_CT_tax, min_id = 82.2) # this is the equivalent of 97 considering the 90 N internal gap
#ITS2_CT_join <- tax_join(ITS2_CT, ITS2_CT_tax, min_id = 92.5)
ITS2_CT_join <- tax_join(ITS2_CT, ITS2_CT_tax, min_id = 95.0)

trnL_eval <- trnL_CT_join %>% group_by(sample) %>%
  summarize(reads = n()) %>%
  arrange(sample)

rbcL_eval <- rbcL_CT_join %>% group_by(sample) %>%
  summarize(reads = n()) %>%
  arrange(sample)

ITS2_eval <- ITS2_CT_join %>% group_by(sample) %>%
  summarize(reads = n()) %>%
  arrange(sample)

reads_eval <- full_join(trnL_eval, rbcL_eval, by = "sample") %>%
  full_join(ITS2_eval, by = "sample")
colnames(reads_eval) <- c("sample", "trnL", "rbcL", "ITS2")
write_csv(reads_eval, "~/vsearchr/inst/extdata/reads_eval.csv")

Tally genera by sample

CT pollen

trnL_CT_tally <- tally_gen(trnL_CT_join)
rbcL_CT_tally <- tally_gen(rbcL_CT_join)
ITS2_CT_tally <- tally_gen(ITS2_CT_join)

Add sample metadata and create consensus data sets

CT pollen

### trnL
trnL_CT_final <- add_meta(trnL_CT_tally, "~/vsearchr/inst/extdata/CT_2015_key.csv")
CT_genus_summary_trnL <- trnL_CT_final %>%
  group_by(genus) %>%
  summarize(gen_freq = n())
CT_trnL_join <- left_join(trnL_CT_final, CT_genus_summary_trnL, by = "genus")

### rbcL
rbcL_CT_final <- add_meta(rbcL_CT_tally, "~/vsearchr/inst/extdata/CT_2015_key.csv")
CT_genus_summary_rbcL <- rbcL_CT_final %>%
  group_by(genus) %>%
  summarize(gen_freq = n())
CT_rbcL_join <- left_join(rbcL_CT_final, CT_genus_summary_rbcL, by = "genus")

### ITS2
ITS2_CT_final <- add_meta(ITS2_CT_tally, "~/vsearchr/inst/extdata/CT_2015_key.csv")
CT_genus_summary_ITS2 <- ITS2_CT_final %>%
  group_by(genus) %>%
  summarize(gen_freq = n())
CT_ITS2_join <- left_join(ITS2_CT_final, CT_genus_summary_ITS2, by = "genus")

### consensus join
CT_consensus <- consensus_xyz_gen(ITS2_CT_final, rbcL_CT_final, trnL_CT_final,
                                  min_prop = 0.0005)
CT_genus_summary_consensus <- CT_consensus %>%
  group_by(genus) %>%
  summarize(gen_freq = n(),
            max_prop = max(scaled_prop))

CT_consensus_final <- left_join(CT_consensus, CT_genus_summary_consensus, by = "genus") %>%
  add_meta("~/vsearchr/inst/extdata/CT_2015_key.csv") %>%
  filter(!sample %in% c("CT12", "CT13", "CT23", "CT27", "CT36")) # exclude samples with < 400 reads for one or more markers

Plot data

trnL only

pdf("~/vsearchr/inst/extdata/figures/CT_metabarcoding_trnL.pdf", width = 8.5, height = 11)
ggplot(filter(CT_trnL_join), aes(x = date, y = reorder(genus, gen_freq), fill = gen_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(8) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

rbcL only

pdf("~/vsearchr/inst/extdata/figures/CT_metabarcoding_rbcL.pdf", width = 8.5, height = 11)
ggplot(filter(CT_rbcL_join), aes(x = date, y = reorder(genus, gen_freq), fill = gen_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(8) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

ITS2 only

pdf("~/vsearchr/inst/extdata/figures/CT_metabarcoding_ITS2.pdf", width = 8.5, height = 11)
ggplot(filter(CT_ITS2_join), aes(x = date, y = reorder(genus, gen_freq), fill = gen_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(8) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

Consensus

### Untrimmed
pdf("~/vsearchr/inst/extdata/figures/CT_metabarcoding_consensus.pdf", width = 8.5, height = 8.5)
ggplot(CT_consensus_final, aes(x = date, y = reorder(genus, gen_freq), fill = scaled_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(10) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

### Filtered to max prop >= 0.05 (to make the plot readable for major taxa)
pdf("~/vsearchr/inst/extdata/figures/CT_metabarcoding_consensus_trim.pdf", width = 8.5, height = 6.5)
ggplot(filter(CT_consensus_final, max_prop >= 0.05), aes(x = date, y = reorder(genus, gen_freq), fill = scaled_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(9) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

Add microscopy data

micro_dat <- read_csv("~/vsearchr/inst/extdata/micro_dat_v2.csv", col_names = TRUE) %>%
  rename(micro_vol_prop = prop_vol,
         micro_ct_prop = prop_count) %>%
  filter(genus != "undet") %>%
  #filter(micro_prop >= 0.001) %>%
  group_by(site, date, genus) %>%
  summarize(micro_vol_prop = sum(micro_vol_prop),
            micro_ct_prop = sum(micro_ct_prop))
CT_genus_summary_micro <- micro_dat %>%
  group_by(genus) %>%
  summarize(gen_freq = n(),
            max_vol_prop = max(micro_vol_prop),
            max_ct_prop = max(micro_ct_prop))
CT_micro_join <- left_join(micro_dat, CT_genus_summary_micro, by = "genus") %>%
  add_meta_micro("~/vsearchr/inst/extdata/CT_2015_key.csv") %>%
  na.omit()

Check whether my Genbank reference libs are missing any genera found in the micro data

micro_anti_trnL <- anti_join(micro_dat, trnL_CT_tax, by = "genus") %>%
  ungroup() %>%
  select(genus) %>%
  unique()

micro_anti_rbcL <- anti_join(micro_dat, rbcL_CT_tax, by = "genus") %>%
  ungroup() %>%
  select(genus) %>%
  unique()

micro_anti_ITS2 <- anti_join(micro_dat, ITS2_CT_tax, by = "genus") %>%
  ungroup() %>%
  select(genus) %>%
  unique()

missing_genera <- bind_rows(micro_anti_trnL, micro_anti_rbcL, micro_anti_ITS2) %>%
  unique() %>%
  arrange(genus)
View(missing_genera)

Join micro and metabarcoding datasets on shared sites dates

mol_dat <- CT_consensus_final %>% ungroup() %>%
  select(sample, site, date, genus, gen_freq, scaled_prop)

shared_sitedates_consensus <- inner_join(CT_micro_join, mol_dat, by = c("site", "date")) %>%
  select(site, date) %>%
  unique()

### join
micromol_dat <- full_join(mol_dat, CT_micro_join, by = c("sample", "site", "date", "genus")) %>%
  semi_join(shared_sitedates_consensus, by = c("site", "date")) %>%
  replace_na(list(scaled_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0, gen_freq.x = 0, gen_freq.y = 0)) %>%
  mutate(shared = case_when(
  scaled_prop == 0 & micro_ct_prop > 0 ~ "micro_only",
  scaled_prop > 0 & micro_ct_prop == 0 ~ "mol_only",
  scaled_prop > 0 | micro_ct_prop > 0 ~ "shared"),
  shared_log = case_when(
    shared == "shared" ~ 1,
    shared != "shared" ~ 0)) %>%
  select(sample, site, date, genus, gen_freq_mol = gen_freq.x, scaled_prop, micro_vol_prop, micro_ct_prop, gen_freq_micro = gen_freq.y, shared, shared_log)

micromol_dat_genus_summary <- micromol_dat %>%
  group_by(genus) %>%
  summarize(gen_freq = n(),
            max_micro_ct = max(micro_ct_prop),
            max_micro_vol = max(micro_vol_prop),
            max_mol = max(scaled_prop))

micromol_dat_final <- left_join(micromol_dat, micromol_dat_genus_summary, by = "genus")
write_csv(micromol_dat_final, "~/Desktop/micro_mol_comparison.csv")

Try joining micro data to ITS2 only

mol_dat_ITS2 <- CT_ITS2_join %>% ungroup() %>%
  select(sample, site, date, genus, gen_prop)

shared_sitedates_consensus_ITS2 <- inner_join(CT_micro_join, mol_dat_ITS2, by = c("site", "date")) %>%
  select(site, date) %>%
  unique()

### join
micromol_dat_ITS2 <- full_join(mol_dat_ITS2, CT_micro_join, by = c("sample", "site", "date", "genus")) %>%
  semi_join(shared_sitedates_consensus_ITS2, by = c("site", "date")) %>%
  replace_na(list(gen_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0)) %>%
  mutate(shared = case_when(
  gen_prop == 0 & micro_ct_prop > 0 ~ "micro_only",
  gen_prop > 0 & micro_ct_prop == 0 ~ "mol_only",
  gen_prop > 0 | micro_ct_prop > 0 ~ "shared"),
  shared_log = case_when(
    shared == "shared" ~ 1,
    shared != "shared" ~ 0)) %>%
  select(sample, site, date, genus, gen_prop, micro_vol_prop, micro_ct_prop, shared, shared_log)

micromol_dat_genus_summary_ITS2 <- micromol_dat_ITS2 %>%
  group_by(genus) %>%
  summarize(gen_freq = n(),
            max_micro_ct = max(micro_ct_prop),
            max_micro_vol = max(micro_vol_prop),
            max_mol = max(gen_prop))

micromol_dat_final_ITS2 <- left_join(micromol_dat_ITS2, micromol_dat_genus_summary_ITS2, by = "genus")
write_csv(micromol_dat_final_ITS2, "~/Desktop/micro_mol_comparison_ITS2.csv")

Plot microscopy data

pdf("~/vsearchr/inst/extdata/figures/CT_micro_major.pdf", width = 8.5, height = 5)
ggplot(filter(CT_micro_join, max_prop >= 0.05), aes(x = date, y = reorder(genus, gen_freq), fill = micro_prop)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(9) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()

Comparing metabarcoding and microscopy

### Bar plot of detections
pdf("~/vsearchr/inst/extdata/figures/CT_mol_v_micro_bar.pdf", width = 8.5, height = 6)
ggplot(micromol_consensus_join, 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  theme_gray(18) +
  scale_fill_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  scale_x_discrete(labels = c("microscopy", "metabarcoding", "both")) +
  ylab("detections") +
  xlab(NULL)
dev.off()

# ITS2 only
ggplot(micromol_dat_final_ITS2, 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  theme_gray(18) +
  scale_fill_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  scale_x_discrete(labels = c("microscopy", "metabarcoding", "both")) +
  ylab("detections") +
  xlab(NULL)

ggplot(filter(micromol_dat_final_ITS2, gen_prop >= 0.05 | micro_vol_prop >= 0.05), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  theme_gray(18) +
  scale_fill_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  scale_x_discrete(labels = c("microscopy", "metabarcoding", "both")) +
  ylab("detections") +
  xlab(NULL)

ggplot(filter(micromol_dat_final_ITS2, gen_prop >= 0.10 | micro_vol_prop >= 0.10), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  theme_gray(18) +
  scale_fill_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  scale_x_discrete(labels = c("microscopy", "metabarcoding", "both")) +
  ylab("detections") +
  xlab(NULL)

### Scatter plot of abundances
pdf("~/vsearchr/inst/extdata/figures/CT_mol_v_micro_trans.pdf", width = 8.5, height = 6)
ggplot(filter(micromol_dat_final), 
       aes(x = sqrt(scaled_prop), y = sqrt(micro_vol_prop), color = shared)) +
  geom_point(alpha = 0.7) +
  geom_smooth(method = "lm") +
  theme_gray(18) +
  geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") +
  scale_color_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  xlab(expression(sqrt("read count"))) +
  ylab(expression(sqrt("grain volume")))
dev.off()

pdf("~/vsearchr/inst/extdata/figures/CT_mol_v_micro_trans.pdf", width = 8.5, height = 6)
ggplot(micromol_dat_final, aes(x = sqrt(scaled_prop), y = sqrt(micro_ct_prop), color = shared)) +
  geom_point(alpha = 0.7) +
  geom_smooth(method = "lm") +
  theme_gray(18) +
  geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") +
  scale_color_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  xlab(expression(sqrt("read count"))) +
  ylab(expression(sqrt("grain count")))
dev.off()

# ITS2 only
ggplot(micromol_dat_final_ITS2, aes(x = sqrt(gen_prop), y = sqrt(micro_ct_prop), color = shared)) +
  geom_point(alpha = 0.7) +
  geom_smooth(method = "lm") +
  theme_gray(18) +
  geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") +
  scale_color_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
  xlab(expression(sqrt("read count"))) +
  ylab(expression(sqrt("grain count")))

### Scatter plot of frequencies
pdf("~/vsearchr/inst/extdata/figures/CT_mol_v_micro_freq.pdf", width = 8.5, height = 6)
ggplot(micromol_dat_final, aes(gen_freq_mol, gen_freq_micro, color = shared)) +
  geom_point(alpha = 0.2) +
  geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") +
  stat_smooth(method = "lm")
dev.off()

### Heatmap of agreement
ggplot(filter(micromol_consensus_join, scaled_prop >= 0.05 | micro_prop >= 0.05), aes(x = date, y = reorder(genus, gen_freq), fill = difference)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "blue", high = "red") +
  theme_bw(9) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Difference") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

ggplot(filter(micromol_consensus_join, scaled_prop >= 0.05 & micro_prop >= 0.05), aes(x = date, y = reorder(genus, gen_freq), fill = difference)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "blue", high = "red") +
  theme_bw(9) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Difference") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

ggplot(filter(micromol_consensus_join, scaled_prop >= 0 & micro_prop > 0), aes(x = date, y = reorder(genus, gen_freq), fill = difference)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "blue", high = "red") +
  theme_bw(9) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Difference") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

### Grouped barplot of agreement
micromol_long <- micromol_dat_final %>% 
  select(sample, site, date, genus, scaled_prop, micro_vol_prop, micro_ct_prop) %>%
  gather(metric, value, -sample, -site, -date, -genus)

ggplot(filter(micromol_long, sample == "CT1"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_8/20") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT2"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_9/17") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0917.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT3"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_7/27") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0727.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT4"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_6/12") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0612.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT5"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/8") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0708.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT6"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/16") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0716.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT7"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_8/31") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0831.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT8"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_9/3") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0903.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT9"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_9/10") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0910.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT10"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_9/2") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0902.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT11"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/15") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0715.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT12"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/2") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0702.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT13"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_5/27") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0527.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT14"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_7/7") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0707.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT15"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0513.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT16"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/4") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0604.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT17"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_8/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0813.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT18"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/23") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0723.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT19"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_8/10") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0810.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT20"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/13") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0813.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT21"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_6/17") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0617.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT22"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_9/23") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0923.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT23"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_6/18") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0618.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT24"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/11") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0611.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT25"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_5/28") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0528.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT26"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/30") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0630.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT27"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_6/24") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0624.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT28"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/22") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0522.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT29"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_9/14") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0914.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT30"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_9/21") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0921.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT31"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/10") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0610.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT32"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_8/3") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0803.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT33"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/25") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0825.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT34"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/29") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0529.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT35"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/22") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0722.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT36"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_8/7") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0807.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT37"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/25") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0625.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT38"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_8/4") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0804.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT39"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_7/30") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0730.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT40"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/19") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0819.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT41"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/3") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/B0603.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT42"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_9/18") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0918.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long, sample == "CT43"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_7/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0713.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT44"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_6/26") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0626.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT45"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_8/28") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0828.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT46"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/19") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/C0619.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long, sample == "CT47"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_7/20") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") +
ggsave("~/vsearchr/inst/extdata/figures/A0720.pdf", width = 6.5, height = 6.5)


### Identifying genera detected by each method
micromol_consensus_join_mol <- filter(micromol_consensus_join, scaled_prop > 0)
micromol_consensus_join_micro <- filter(micromol_consensus_join, micro_prop > 0)
shared_genera <- inner_join(micromol_consensus_join_mol, micromol_consensus_join_micro, by = "genus") %>%
  select(genus) %>%
  unique()
mol_genera <- micromol_consensus_join_mol %>% 
  select(genus) %>%
  unique()
micro_genera <- micromol_consensus_join_micro %>% 
  select(genus) %>%
  unique()

length(shared_genera$genus) / (length(mol_genera$genus) + length(micro_genera$genus))

length(filter(micromol_consensus_join, shared == "mol_only")$genus)
length(filter(micromol_consensus_join, shared == "micro_only")$genus)
length(filter(micromol_consensus_join, shared == "shared")$genus)

length(unique(filter(micromol_consensus_join, shared == "mol_only")$genus))
length(unique(filter(micromol_consensus_join, shared == "micro_only")$genus))
length(unique(filter(micromol_consensus_join, shared == "shared")$genus))

### Linear model of abundance
lm1 <- lm(micro_prop ~ scaled_prop, data = filter(micromol_consensus_join, shared == "shared"))
summary(lm1)

### Count proportion vs volume proportion
ggplot(micromol_dat_final, aes(micro_ct_prop, micro_vol_prop)) +
  geom_point() +
  stat_smooth(method = "lm")

ggplot(micromol_dat_final, aes(sqrt(micro_ct_prop), sqrt(micro_vol_prop))) +
  geom_point() +
  stat_smooth(method = "lm") +
  xlab("sqrt(count)") +
  ylab("sqrt(volume)")
ggsave("~/Desktop/count_vs_volume.pdf")

Side-by-side barplots ITS2 only

micromol_long_ITS2 <- micromol_dat_final_ITS2 %>% 
  select(sample, site, date, genus, gen_prop, micro_vol_prop, micro_ct_prop) %>%
  gather(metric, value, -sample, -site, -date, -genus)

ggplot(filter(micromol_long_ITS2, sample == "CT1"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_8/20") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT2"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_9/17") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/B0917.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT3"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_7/27") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0727.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT4"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_6/12") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0612.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT5"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/8") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/B0708.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT6"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/16") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0716.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT7"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_8/31") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/A0831.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT8"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_9/3") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/C0903.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT9"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_9/10") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0910.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT10"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_9/2") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0902.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT11"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/15") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
 # scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0715.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT12"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/2") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0702.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT13"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_5/27") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0527.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT14"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_7/7") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0707.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT15"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0513.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT16"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/4") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/C0604.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT17"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_8/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0813.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT18"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_7/23") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0723.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT19"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_8/10") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0810.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT20"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/13") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/B0813.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT21"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_6/17") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0617.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT22"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_9/23") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0923.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT23"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_6/18") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0618.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT24"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/11") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0611.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT25"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_5/28") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/C0528.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT26"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/30") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance") 
ggsave("~/vsearchr/inst/extdata/figures/B0630.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT27"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_6/24") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0624.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT28"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/22") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0522.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT29"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_9/14") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0914.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT30"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_9/21") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0921.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT31"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/10") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0610.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT32"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_8/3") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0803.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT33"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/25") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0825.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT34"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_5/29") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0529.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT35"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_7/22") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0722.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT36"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_8/7") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0807.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT37"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/25") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0625.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT38"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("B_8/4") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0804.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT39"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_7/30") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0730.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT40"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_8/19") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0819.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT41"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("B_6/3") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0603.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT42"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("C_9/18") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0918.pdf", width = 6.5, height = 6.5)

# ggplot(filter(micromol_long_ITS2, sample == "CT43"), aes(x = genus, y = value, fill = metric)) +
#   geom_bar(stat = "identity", position = "dodge") +
#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
#   ggtitle("A_7/13") +
#   geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
#   scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
#   ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0713.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT44"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_6/26") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0626.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT45"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_8/28") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0828.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT46"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("C_6/19") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0619.pdf", width = 6.5, height = 6.5)

ggplot(filter(micromol_long_ITS2, sample == "CT47"), aes(x = genus, y = value, fill = metric)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("A_7/20") +
  geom_abline(intercept = 0.05, slope = 0, color = "gray40", linetype = "dashed") +
  #scale_fill_discrete(name = NULL, labels = c("microscopy (vol)", "microcopy (ct)", "metabarcoding")) +
  ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0720.pdf", width = 6.5, height = 6.5)

ggplot(micromol_consensus, aes(x = shared, fill = shared)) +
  geom_bar() +
  theme_gray(8) 
# +
#   facet_grid(site ~ date)

ggplot(filter(micromol_consensus, scaled_prop >= 0.01), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8)

ggplot(filter(micromol_consensus, scaled_prop >= 0.04), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8)
# +
#   facet_grid(site ~ date)

ggplot(filter(micromol_consensus, scaled_prop >= 0.05), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8)

ggplot(filter(micromol_consensus, scaled_prop >= 0.10), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8) 
# +
#   facet_wrap(. ~ site)

ggplot(filter(micromol_consensus, scaled_prop >= 0.25), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8)
# +
#   facet_grid(site ~ date) 

ggplot(filter(micromol_consensus, scaled_prop >= 0.35), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8) 
# +
#   facet_grid(site ~ date) 

ggplot(filter(micromol_consensus, scaled_prop >= 0.50), 
       aes(x = shared, fill = shared)) +
  geom_bar() +
  geom_bar() +
  theme_gray(8)
# +
#   facet_grid(site ~ date) 


micro_genera <- tibble(unique(micro_dat$genus)) %>%
  select(genus = 1)

mol_genera <- tibble(unique(CT_consensus_final$genus)) %>%
  select(genus = 1)

anti_join(micro_genera, mol_genera)

anti_join(mol_genera, micro_genera)


ggplot(micromol_consensus, aes(x = scaled_prop, y = shared_log)) +
  geom_point() +
  geom_smooth()

ggplot(micromol_consensus, aes(x = gen_freq_mol, y = shared_log)) +
  geom_point() +
  geom_smooth()

Plot shared genera only

ggplot(filter(micromol_consensus, shared == "shared"), 
       aes(x = date, y = genus)) +
  geom_tile(width = 6, color = "black") +
  scale_fill_gradient(low = "gray95", high = "purple") +
  theme_bw(8) +
  ylab("Genus") +
  xlab("Sample") +
  labs(fill = "Proportional\nabundance") +
  facet_grid(~site) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

pdf("~/vsearchr/inst/extdata/figures/CT_genus_hist.pdf", width = 7.5, height = 5)
ggplot(CT_genus_summary_consensus, aes(reorder(genus, -gen_freq), gen_freq)) +
  geom_histogram(stat = "identity") +
  xlab("genus") +
  ylab("frequency") +
  theme_gray(8) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
dev.off()