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/")
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")
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")
trnL_CT_tally <- tally_gen(trnL_CT_join) rbcL_CT_tally <- tally_gen(rbcL_CT_join) ITS2_CT_tally <- tally_gen(ITS2_CT_join)
### 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
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()
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()
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()
### 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()
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()
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)
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")
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")
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()
### 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")
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()
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()
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