In sponslerdb/vsearchR:
Load vsearch output
CT pollen
rbcL <- load_blast6("~/vsearchr/inst/extdata/rbcL_vsearch_CT.output/outs/")
### Check for short but high ID alignments
rbcL_98 <- filter(rbcL, pident >= 82.8)
rbcL_97 <- filter(rbcL, pident >= 81.9)
rbcL_96 <- filter(rbcL, pident >= 81.1)
rbcL_95 <- filter(rbcL, pident >= 79.4)
rbcL_94 <- filter(rbcL, pident >= 78.5)
rbcL_92 <- filter(rbcL, pident >= 77.7)
Load taxonomy tables
CT pollen
rbcL_tax <- load_MTXA("~/vsearchr/inst/extdata/rbcL_CT_Amplicons.tax")
Join vsearch output to taxonomy tables
CT pollen
rbcL_join_98 <- tax_join(rbcL, rbcL_tax, min_id = 82.8, min_len = 300)
rbcL_eval_98 <- rbcL_join_98 %>% group_by(sample) %>%
summarize(reads = n()) %>%
arrange(sample)
rbcL_join_92 <- tax_join(rbcL, rbcL_tax, min_id = 77.7, min_len = 300) %>%
rbcL_eval_92 <- rbcL_join_92 %>% group_by(sample) %>%
summarize(reads = n()) %>%
arrange(sample)
Tally genera by sample
CT pollen
rbcL_tally_98 <- tally_gen(rbcL_join_98) %>%
mutate(sample_mod = str_extract(sample, "^[^_]+(?=_)"))
rbcL_tally_92 <- tally_fam(rbcL_join_92) %>%
mutate(sample_mod = str_extract(sample, "^[^_]+(?=_)"))
Add sample metadata and create consensus data sets
CT pollen
### rbcL
rbcL_meta_98 <- add_meta_rbcL(rbcL_tally_98, "~/vsearchr/inst/extdata/CT_2015_key.csv")
genus_summary_rbcL_98 <- rbcL_meta_98 %>%
group_by(genus) %>%
summarize(mol_freq = n(),
max_prop = max(gen_prop))
rbcL_final_98 <- left_join(rbcL_meta_98, genus_summary_rbcL_98, by = "genus")
rbcL_meta_92 <- add_meta_rbcL(rbcL_tally_92, "~/vsearchr/inst/extdata/CT_2015_key.csv")
family_summary_rbcL_92 <- rbcL_meta_92 %>%
group_by(family) %>%
summarize(mol_freq = n(),
max_prop = max(fam_prop))
rbcL_final_92 <- left_join(rbcL_meta_92, family_summary_rbcL_92, by = "family")
Plot data
rbcL only
ggplot(filter(rbcL_final_98, max_prop >= 0.05), aes(x = date, y = reorder(genus, mol_freq), fill = gen_prop)) +
geom_tile(width = 6, color = "black") +
scale_fill_gradient(low = "gray95", high = "purple") +
theme_bw(6) +
ylab("Genus") +
xlab("Sample") +
labs(fill = "Proportional\nabundance") +
facet_grid(~site) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
ggsave("~/vsearchr/inst/extdata/figures/rbcL_98_tileplot.pdf", width = 6.5, height = 4.5)
ggplot(filter(rbcL_final_92, max_prop >= 0.05), aes(x = date, y = reorder(family, mol_freq), fill = gen_prop)) +
geom_tile(width = 6, color = "black") +
scale_fill_gradient(low = "gray95", high = "purple") +
theme_bw(6) +
ylab("Genus") +
xlab("Sample") +
labs(fill = "Proportional\nabundance") +
facet_grid(~site) +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
ggsave("~/vsearchr/inst/extdata/figures/rbcL_92_tileplot.pdf", width = 6.5, height = 4.5)
Add microscopy data
micro_dat_98 <- 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))
micro_dat_92 <- read_csv("~/vsearchr/inst/extdata/micro_dat_v2.csv", col_names = TRUE) %>%
rename(micro_vol_prop = prop_vol,
micro_ct_prop = prop_count) %>%
filter(family != "undet") %>%
#filter(micro_prop >= 0.001) %>%
group_by(site, date, family) %>%
summarize(micro_vol_prop = sum(micro_vol_prop),
micro_ct_prop = sum(micro_ct_prop))
CT_genus_summary_micro <- micro_dat_98 %>%
group_by(genus) %>%
summarize(micro_freq = n(),
max_vol_prop = max(micro_vol_prop),
max_ct_prop = max(micro_ct_prop))
CT_family_summary_micro <- micro_dat_92 %>%
group_by(family) %>%
summarize(micro_freq = n(),
max_vol_prop = max(micro_vol_prop),
max_ct_prop = max(micro_ct_prop))
CT_micro_join_98 <- left_join(micro_dat_98, CT_genus_summary_micro, by = "genus") %>%
add_meta_micro("~/vsearchr/inst/extdata/CT_2015_key.csv") %>%
na.omit()
CT_micro_join_92 <- left_join(micro_dat_92, CT_family_summary_micro, by = "family") %>%
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_rbcL <- anti_join(micro_dat, rbcL_tax, by = "genus") %>%
ungroup() %>%
select(genus) %>%
unique()
Join micro and metabarcoding data
mol_dat_98 <- rbcL_final_98 %>%
ungroup() %>%
select(sample = sample_mod, site, date, genus, gen_prop, max_prop, mol_freq)
mol_dat_92 <- rbcL_final_92 %>%
ungroup() %>%
select(sample = sample_mod, site, date, family, fam_prop, max_prop, mol_freq)
shared_sitedates <- inner_join(CT_micro_join_98, mol_dat_98, by = c("site", "date")) %>%
select(site, date) %>%
unique()
### join
micromol_dat_98 <- full_join(mol_dat_98, CT_micro_join_98, by = c("sample", "site", "date", "genus")) %>%
semi_join(shared_sitedates, by = c("site", "date")) %>%
replace_na(list(gen_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0, mol_freq = 0, micro_freq = 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, max_prop, micro_vol_prop, micro_ct_prop, shared, shared_log, mol_freq, micro_freq)
micromol_dat_genus_summary_98 <- micromol_dat_98 %>%
group_by(genus) %>%
summarize(max_micro_ct = max(micro_ct_prop),
max_micro_vol = max(micro_vol_prop))
micromol_dat_final_98 <- left_join(micromol_dat_98, micromol_dat_genus_summary_98, by = "genus")
write_csv(micromol_dat_final_98, "~/Desktop/micro_mol_comparison_rbcL_98.csv")
micromol_dat_92 <- full_join(mol_dat_92, CT_micro_join_92, by = c("sample", "site", "date", "family")) %>%
semi_join(shared_sitedates, by = c("site", "date")) %>%
replace_na(list(fam_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0, mol_freq = 0, micro_freq = 0)) %>%
mutate(shared = case_when(
fam_prop == 0 & micro_ct_prop > 0 ~ "micro_only",
fam_prop > 0 & micro_ct_prop == 0 ~ "mol_only",
fam_prop > 0 | micro_ct_prop > 0 ~ "shared"),
shared_log = case_when(
shared == "shared" ~ 1,
shared != "shared" ~ 0)) %>%
select(sample, site, date, family, fam_prop, max_prop, micro_vol_prop, micro_ct_prop, shared, shared_log, mol_freq, micro_freq)
micromol_dat_family_summary_92 <- micromol_dat_92 %>%
group_by(family) %>%
summarize(max_micro_ct = max(micro_ct_prop),
max_micro_vol = max(micro_vol_prop))
micromol_dat_final_92 <- left_join(micromol_dat_92, micromol_dat_family_summary_92, by = "family")
write_csv(micromol_dat_final_92, "~/Desktop/micro_mol_comparison_rbcL_92.csv")
Plot microscopy data
ggplot(filter(CT_micro_join, max_vol_prop >= 0.05), aes(x = date, y = reorder(genus, micro_freq), fill = micro_vol_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))
ggsave("~/vsearchr/inst/extdata/figures/micro_tileplot.pdf", width = 7.5, height = 4.5)
ggsave("~/vsearchr/inst/extdata/figures/micro_tileplot.png", width = 7.5, height = 4.5)
Comparing metabarcoding and microscopy
### Bar plot of detections
# rbcL only
ggplot(micromol_dat_final_98, 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(micromol_dat_final_92, 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_98, gen_prop >= 0.05 | micro_vol_prop >= 0.05),
aes(x = shared, fill = shared)) +
geom_bar() +
theme_gray(14) +
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_92, fam_prop >= 0.05 | micro_vol_prop >= 0.05),
aes(x = shared, fill = shared)) +
geom_bar() +
theme_gray(14) +
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_92, fam_prop >= 0.05 | micro_vol_prop >= 0.05),
aes(x = shared, fill = shared)) +
geom_bar() +
theme_gray(14) +
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
#### Grain count
ggplot(micromol_dat_final_98, aes(x = sqrt(gen_prop), y = sqrt(micro_ct_prop), color = shared)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "lm") +
theme_gray(14) +
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")))
ggplot(micromol_dat_final_92, aes(x = sqrt(fam_prop), y = sqrt(micro_ct_prop), color = shared)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "lm") +
theme_gray(14) +
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")))
#### Volume
ggplot(micromol_dat_final_98, aes(x = sqrt(gen_prop), y = sqrt(micro_vol_prop), color = shared)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "lm") +
theme_gray(14) +
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")))
ggplot(micromol_dat_final_92, aes(x = sqrt(fam_prop), y = sqrt(micro_vol_prop), color = shared)) +
geom_point(alpha = 0.7) +
geom_smooth(method = "lm") +
theme_gray(14) +
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
ggplot(micromol_dat_final, aes(mol_freq, micro_freq, color = shared)) +
geom_point(alpha = 0.2) +
theme_gray(14) +
geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") +
scale_color_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) +
stat_smooth(method = "lm")
ggsave("~/vsearchr/inst/extdata/figures/micro_vs_mol_freq.pdf", width = 6.5, height = 4)
ggsave("~/vsearchr/inst/extdata/figures/micro_vs_mol_freq.png", width = 6.5, height = 4)
### Grouped barplot of agreement
micromol_long <- micromol_dat_final %>%
select(sample, site, date, genus, gen_prop, micro_vol_prop) %>%
gather(metric, value, -sample, -site, -date, -genus)
micromol_long_major <- micromol_dat_final %>%
filter(gen_prop >= 0.05 | micro_ct_prop >= 0.05) %>%
select(sample, site, date, genus, gen_prop, micro_vol_prop) %>%
gather(metric, value, -sample, -site, -date, -genus)
ggplot(micromol_long_major, aes(x = genus, y = value, fill = metric)) +
geom_bar(stat = "identity", position = "dodge") +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_discrete(name = NULL, labels = c("metabarcoding", "microcopy")) +
ylab("proportional abundance") +
facet_grid(sample ~ .)
ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0917.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0727.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0612.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0708.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0716.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0831.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0903.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0910.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0902.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0715.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0702.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0527.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0707.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0513.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0604.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0813.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0723.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0810.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0813.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0617.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0923.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0618.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0611.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0528.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0630.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0624.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0522.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0914.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0921.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0610.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0803.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0825.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0529.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0722.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0807.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0625.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/B0804.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0730.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0819.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/B0603.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/C0918.pdf", width = 6.5, height = 6.5)
# ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
# ylab("proportional abundance") +
# ggsave("~/vsearchr/inst/extdata/figures/A0713.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0626.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0828.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/C0619.pdf", width = 6.5, height = 6.5)
ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) +
ylab("proportional abundance")
ggsave("~/vsearchr/inst/extdata/figures/A0720.pdf", width = 6.5, height = 6.5)
### Linear model of abundance
lm1 <- lm(sqrt(micro_vol_prop) ~ sqrt(gen_prop), data = filter(micromol_dat_final, shared_log == 1))
summary(lm1)
plot(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")
# Unique genera detected
micro_genera_major <- tibble(unique(filter(micro_dat, micro_vol_prop >= 0.05)$genus)) %>% rename(genus = 1)
mol_genera_major <- tibble(unique(filter(rbcL_final, gen_prop >= 0.05)$genus)) %>% rename(genus = 1)
shared_genera_major <- inner_join(micro_genera_major, mol_genera_major)
sponslerdb/vsearchR documentation built on June 19, 2020, 10:01 a.m.
R Package Documentation
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Load vsearch output
CT pollen
rbcL <- load_blast6("~/vsearchr/inst/extdata/rbcL_vsearch_CT.output/outs/") ### Check for short but high ID alignments rbcL_98 <- filter(rbcL, pident >= 82.8) rbcL_97 <- filter(rbcL, pident >= 81.9) rbcL_96 <- filter(rbcL, pident >= 81.1) rbcL_95 <- filter(rbcL, pident >= 79.4) rbcL_94 <- filter(rbcL, pident >= 78.5) rbcL_92 <- filter(rbcL, pident >= 77.7)
Load taxonomy tables
CT pollen
rbcL_tax <- load_MTXA("~/vsearchr/inst/extdata/rbcL_CT_Amplicons.tax")
Join vsearch output to taxonomy tables
CT pollen
rbcL_join_98 <- tax_join(rbcL, rbcL_tax, min_id = 82.8, min_len = 300) rbcL_eval_98 <- rbcL_join_98 %>% group_by(sample) %>% summarize(reads = n()) %>% arrange(sample) rbcL_join_92 <- tax_join(rbcL, rbcL_tax, min_id = 77.7, min_len = 300) %>% rbcL_eval_92 <- rbcL_join_92 %>% group_by(sample) %>% summarize(reads = n()) %>% arrange(sample)
Tally genera by sample
CT pollen
rbcL_tally_98 <- tally_gen(rbcL_join_98) %>% mutate(sample_mod = str_extract(sample, "^[^_]+(?=_)")) rbcL_tally_92 <- tally_fam(rbcL_join_92) %>% mutate(sample_mod = str_extract(sample, "^[^_]+(?=_)"))
Add sample metadata and create consensus data sets
CT pollen
### rbcL rbcL_meta_98 <- add_meta_rbcL(rbcL_tally_98, "~/vsearchr/inst/extdata/CT_2015_key.csv") genus_summary_rbcL_98 <- rbcL_meta_98 %>% group_by(genus) %>% summarize(mol_freq = n(), max_prop = max(gen_prop)) rbcL_final_98 <- left_join(rbcL_meta_98, genus_summary_rbcL_98, by = "genus") rbcL_meta_92 <- add_meta_rbcL(rbcL_tally_92, "~/vsearchr/inst/extdata/CT_2015_key.csv") family_summary_rbcL_92 <- rbcL_meta_92 %>% group_by(family) %>% summarize(mol_freq = n(), max_prop = max(fam_prop)) rbcL_final_92 <- left_join(rbcL_meta_92, family_summary_rbcL_92, by = "family")
Plot data
rbcL only
ggplot(filter(rbcL_final_98, max_prop >= 0.05), aes(x = date, y = reorder(genus, mol_freq), fill = gen_prop)) + geom_tile(width = 6, color = "black") + scale_fill_gradient(low = "gray95", high = "purple") + theme_bw(6) + ylab("Genus") + xlab("Sample") + labs(fill = "Proportional\nabundance") + facet_grid(~site) + theme(axis.text.x = element_text(angle = 45, hjust = 1)) ggsave("~/vsearchr/inst/extdata/figures/rbcL_98_tileplot.pdf", width = 6.5, height = 4.5) ggplot(filter(rbcL_final_92, max_prop >= 0.05), aes(x = date, y = reorder(family, mol_freq), fill = gen_prop)) + geom_tile(width = 6, color = "black") + scale_fill_gradient(low = "gray95", high = "purple") + theme_bw(6) + ylab("Genus") + xlab("Sample") + labs(fill = "Proportional\nabundance") + facet_grid(~site) + theme(axis.text.x = element_text(angle = 45, hjust = 1)) ggsave("~/vsearchr/inst/extdata/figures/rbcL_92_tileplot.pdf", width = 6.5, height = 4.5)
Add microscopy data
micro_dat_98 <- 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)) micro_dat_92 <- read_csv("~/vsearchr/inst/extdata/micro_dat_v2.csv", col_names = TRUE) %>% rename(micro_vol_prop = prop_vol, micro_ct_prop = prop_count) %>% filter(family != "undet") %>% #filter(micro_prop >= 0.001) %>% group_by(site, date, family) %>% summarize(micro_vol_prop = sum(micro_vol_prop), micro_ct_prop = sum(micro_ct_prop)) CT_genus_summary_micro <- micro_dat_98 %>% group_by(genus) %>% summarize(micro_freq = n(), max_vol_prop = max(micro_vol_prop), max_ct_prop = max(micro_ct_prop)) CT_family_summary_micro <- micro_dat_92 %>% group_by(family) %>% summarize(micro_freq = n(), max_vol_prop = max(micro_vol_prop), max_ct_prop = max(micro_ct_prop)) CT_micro_join_98 <- left_join(micro_dat_98, CT_genus_summary_micro, by = "genus") %>% add_meta_micro("~/vsearchr/inst/extdata/CT_2015_key.csv") %>% na.omit() CT_micro_join_92 <- left_join(micro_dat_92, CT_family_summary_micro, by = "family") %>% 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_rbcL <- anti_join(micro_dat, rbcL_tax, by = "genus") %>% ungroup() %>% select(genus) %>% unique()
Join micro and metabarcoding data
mol_dat_98 <- rbcL_final_98 %>% ungroup() %>% select(sample = sample_mod, site, date, genus, gen_prop, max_prop, mol_freq) mol_dat_92 <- rbcL_final_92 %>% ungroup() %>% select(sample = sample_mod, site, date, family, fam_prop, max_prop, mol_freq) shared_sitedates <- inner_join(CT_micro_join_98, mol_dat_98, by = c("site", "date")) %>% select(site, date) %>% unique() ### join micromol_dat_98 <- full_join(mol_dat_98, CT_micro_join_98, by = c("sample", "site", "date", "genus")) %>% semi_join(shared_sitedates, by = c("site", "date")) %>% replace_na(list(gen_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0, mol_freq = 0, micro_freq = 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, max_prop, micro_vol_prop, micro_ct_prop, shared, shared_log, mol_freq, micro_freq) micromol_dat_genus_summary_98 <- micromol_dat_98 %>% group_by(genus) %>% summarize(max_micro_ct = max(micro_ct_prop), max_micro_vol = max(micro_vol_prop)) micromol_dat_final_98 <- left_join(micromol_dat_98, micromol_dat_genus_summary_98, by = "genus") write_csv(micromol_dat_final_98, "~/Desktop/micro_mol_comparison_rbcL_98.csv") micromol_dat_92 <- full_join(mol_dat_92, CT_micro_join_92, by = c("sample", "site", "date", "family")) %>% semi_join(shared_sitedates, by = c("site", "date")) %>% replace_na(list(fam_prop = 0, micro_vol_prop = 0, micro_ct_prop = 0, mol_freq = 0, micro_freq = 0)) %>% mutate(shared = case_when( fam_prop == 0 & micro_ct_prop > 0 ~ "micro_only", fam_prop > 0 & micro_ct_prop == 0 ~ "mol_only", fam_prop > 0 | micro_ct_prop > 0 ~ "shared"), shared_log = case_when( shared == "shared" ~ 1, shared != "shared" ~ 0)) %>% select(sample, site, date, family, fam_prop, max_prop, micro_vol_prop, micro_ct_prop, shared, shared_log, mol_freq, micro_freq) micromol_dat_family_summary_92 <- micromol_dat_92 %>% group_by(family) %>% summarize(max_micro_ct = max(micro_ct_prop), max_micro_vol = max(micro_vol_prop)) micromol_dat_final_92 <- left_join(micromol_dat_92, micromol_dat_family_summary_92, by = "family") write_csv(micromol_dat_final_92, "~/Desktop/micro_mol_comparison_rbcL_92.csv")
Plot microscopy data
ggplot(filter(CT_micro_join, max_vol_prop >= 0.05), aes(x = date, y = reorder(genus, micro_freq), fill = micro_vol_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)) ggsave("~/vsearchr/inst/extdata/figures/micro_tileplot.pdf", width = 7.5, height = 4.5) ggsave("~/vsearchr/inst/extdata/figures/micro_tileplot.png", width = 7.5, height = 4.5)
Comparing metabarcoding and microscopy
### Bar plot of detections # rbcL only ggplot(micromol_dat_final_98, 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(micromol_dat_final_92, 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_98, gen_prop >= 0.05 | micro_vol_prop >= 0.05), aes(x = shared, fill = shared)) + geom_bar() + theme_gray(14) + 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_92, fam_prop >= 0.05 | micro_vol_prop >= 0.05), aes(x = shared, fill = shared)) + geom_bar() + theme_gray(14) + 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_92, fam_prop >= 0.05 | micro_vol_prop >= 0.05), aes(x = shared, fill = shared)) + geom_bar() + theme_gray(14) + 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 #### Grain count ggplot(micromol_dat_final_98, aes(x = sqrt(gen_prop), y = sqrt(micro_ct_prop), color = shared)) + geom_point(alpha = 0.7) + geom_smooth(method = "lm") + theme_gray(14) + 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"))) ggplot(micromol_dat_final_92, aes(x = sqrt(fam_prop), y = sqrt(micro_ct_prop), color = shared)) + geom_point(alpha = 0.7) + geom_smooth(method = "lm") + theme_gray(14) + 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"))) #### Volume ggplot(micromol_dat_final_98, aes(x = sqrt(gen_prop), y = sqrt(micro_vol_prop), color = shared)) + geom_point(alpha = 0.7) + geom_smooth(method = "lm") + theme_gray(14) + 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"))) ggplot(micromol_dat_final_92, aes(x = sqrt(fam_prop), y = sqrt(micro_vol_prop), color = shared)) + geom_point(alpha = 0.7) + geom_smooth(method = "lm") + theme_gray(14) + 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 ggplot(micromol_dat_final, aes(mol_freq, micro_freq, color = shared)) + geom_point(alpha = 0.2) + theme_gray(14) + geom_abline(intercept = 0, slope = 1, color = "gray40", linetype = "dashed") + scale_color_discrete(name = NULL, labels = c("microscopy", "metabarcoding", "both")) + stat_smooth(method = "lm") ggsave("~/vsearchr/inst/extdata/figures/micro_vs_mol_freq.pdf", width = 6.5, height = 4) ggsave("~/vsearchr/inst/extdata/figures/micro_vs_mol_freq.png", width = 6.5, height = 4) ### Grouped barplot of agreement micromol_long <- micromol_dat_final %>% select(sample, site, date, genus, gen_prop, micro_vol_prop) %>% gather(metric, value, -sample, -site, -date, -genus) micromol_long_major <- micromol_dat_final %>% filter(gen_prop >= 0.05 | micro_ct_prop >= 0.05) %>% select(sample, site, date, genus, gen_prop, micro_vol_prop) %>% gather(metric, value, -sample, -site, -date, -genus) ggplot(micromol_long_major, aes(x = genus, y = value, fill = metric)) + geom_bar(stat = "identity", position = "dodge") + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_discrete(name = NULL, labels = c("metabarcoding", "microcopy")) + ylab("proportional abundance") + facet_grid(sample ~ .) ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0820.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0917.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0727.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0612.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0708.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/C0716.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0831.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0903.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/C0910.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0902.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0715.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0702.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/B0527.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0707.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0513.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0604.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/C0813.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0723.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0810.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0813.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/B0617.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/B0923.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0618.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0611.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0528.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0630.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/B0624.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0522.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0914.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0921.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0610.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0803.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0825.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0529.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0722.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0807.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0625.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/B0804.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0730.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0819.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/B0603.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/C0918.pdf", width = 6.5, height = 6.5) # ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + # ylab("proportional abundance") + # ggsave("~/vsearchr/inst/extdata/figures/A0713.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0626.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0828.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/C0619.pdf", width = 6.5, height = 6.5) ggplot(filter(micromol_long_major, 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("metabarcoding", "microcopy (vol)")) + ylab("proportional abundance") ggsave("~/vsearchr/inst/extdata/figures/A0720.pdf", width = 6.5, height = 6.5) ### Linear model of abundance lm1 <- lm(sqrt(micro_vol_prop) ~ sqrt(gen_prop), data = filter(micromol_dat_final, shared_log == 1)) summary(lm1) plot(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") # Unique genera detected micro_genera_major <- tibble(unique(filter(micro_dat, micro_vol_prop >= 0.05)$genus)) %>% rename(genus = 1) mol_genera_major <- tibble(unique(filter(rbcL_final, gen_prop >= 0.05)$genus)) %>% rename(genus = 1) shared_genera_major <- inner_join(micro_genera_major, mol_genera_major)
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