In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

Test plot_tax_bar()

Import and clean data

# Import Data

library(tidyverse)
theme_set(theme_bw())
library(phyloseq)
devtools::load_all('~/Projects/Mine/aftersl1p/')

load('~/Projects/Mine/aftersl1p/benchmark/data.RData')

seqs = rownames(asv_tab)
all(seqs == rownames(tax_tab))
rownames(asv_tab) = rownames(tax_tab) = NULL

rownames(map_tab) = map_tab$SampleID

setdiff(colnames(asv_tab), rownames(map_tab))
asv_tab = as.matrix(asv_tab)
tax_tab = as.matrix(tax_tab)
dat = phyloseq(otu_table(asv_tab, taxa_are_rows = TRUE),
               tax_table(tax_tab),
               sample_data(map_tab))

# Clean Data
dat
dat = prop_tax_down(dat, indic = FALSE)
dat_rel = transform_sample_counts(dat, function(x) x/sum(x))
keep = taxa_sums(dat)/nsamples(dat) >= 100
dat_filt = prune_taxa(keep, dat)
dat_rel_filt = prune_taxa(keep, dat_rel)

Taxa Bar Charts

• ~~All taxonomic ranks~~
• ~~leglen options:~~
  • ~~NULL~~
  • ~~> n_taxa~~
  • ~~0 < leglen < n_taxa~~
  • ~~0~~
  • ~~< 0~~
  • ~~not a number~~
• legloc options:
  • ~~top~~
  • ~~bottom~~
  • ~~right~~
  • ~~left~~
  • ~~none~~
  • ~~bad~~
• provide own colour vector
  • ~~named (good)~~
  • ~~named (bad)~~
  • ~~named (too short)~~
  • ~~unnamed (long enough)~~
  • ~~unnamed (not long enough)~~
• ~~rotate ticks~~
• ~~means~~

All taxonomic ranks

Kingdom

king_df = make_phy_df(dat_rel_filt, 'Kingdom', prop = FALSE)
king_plt = plot_tax_bar(king_df, 'Kingdom', sample = 'SampleID')
king_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/king_plt.pdf',
       width = 10, height = 5)

Phylum

phy_df = make_phy_df(dat_rel_filt, 'Phylum', prop = FALSE)
phy_plt = plot_tax_bar(phy_df, 'Phylum', sample = 'SampleID')
phy_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/phy_plt.pdf',
       width = 10, height = 5)

plot_tax_bar(phy_df, 'Kingdom', sample = 'SampleID')

Class

class_df = make_phy_df(dat_rel_filt, 'Class', prop = FALSE)
class_plt = plot_tax_bar(class_df, 'Class', sample = 'SampleID')
class_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/class_plt.pdf',
       width = 10, height = 5)
plot_tax_bar(class_df, 'Phylum', sample = 'SampleID')
plot_tax_bar(class_df, 'Kingdom', sample = 'SampleID')

Order

ord_df = make_phy_df(dat_rel_filt, 'Order', prop = FALSE)
ord_plt = plot_tax_bar(ord_df, 'Order', sample = 'SampleID')
ord_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/ord_plt.pdf',
       width = 10, height = 5)
plot_tax_bar(ord_df, 'Class', sample = 'SampleID')
plot_tax_bar(ord_df, 'Phylum', sample = 'SampleID')
plot_tax_bar(ord_df, 'Kingdom', sample = 'SampleID')

Family

fam_df = make_phy_df(dat_rel_filt, 'Family', prop = FALSE)
fam_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID')
fam_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/fam_plt.pdf',
       width = 10, height = 5)
plot_tax_bar(fam_df, 'Order', sample = 'SampleID')
plot_tax_bar(fam_df, 'Class', sample = 'SampleID')
plot_tax_bar(fam_df, 'Phylum', sample = 'SampleID')
plot_tax_bar(fam_df, 'Kingdom', sample = 'SampleID')

Genus

gen_df = make_phy_df(dat_rel_filt, 'Genus', prop = FALSE)
gen_plt = plot_tax_bar(gen_df, 'Genus', sample = 'SampleID')
gen_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/gen_plt.pdf',
       width = 10, height = 5)
plot_tax_bar(gen_df, 'Family', sample = 'SampleID')
plot_tax_bar(gen_df, 'Order', sample = 'SampleID')
plot_tax_bar(gen_df, 'Class', sample = 'SampleID')
plot_tax_bar(gen_df, 'Phylum', sample = 'SampleID')
plot_tax_bar(gen_df, 'Kingdom', sample = 'SampleID')

Species

spec_df = make_phy_df(dat_rel_filt, 'Species', prop = FALSE)
spec_plt = plot_tax_bar(spec_df, 'Species', sample = 'SampleID')
spec_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/spec_plt.pdf',
       width = 10, height = 5)
plot_tax_bar(spec_df, 'Genus', sample = 'SampleID')
plot_tax_bar(spec_df, 'Family', sample = 'SampleID')
plot_tax_bar(spec_df, 'Order', sample = 'SampleID')
plot_tax_bar(spec_df, 'Class', sample = 'SampleID')
plot_tax_bar(spec_df, 'Phylum', sample = 'SampleID')
plot_tax_bar(spec_df, 'Kingdom', sample = 'SampleID')

Leglen Options

NULL

null_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = NULL)
null_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/null_plt.pdf',
       width = 10, height = 5)

> n_taxa

too_big_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', 
                           leglen = n_distinct(fam_df$Family) + 2)
too_big_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/too_big_plt.pdf',
       width = 10, height = 5)

0 < leglen < n_taxa

sml_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', 
                           leglen = round(n_distinct(fam_df$Family)/2))
sml_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/sml_plt.pdf',
       width = 10, height = 5)

0

zero_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', 
                           leglen = 0)
zero_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/zero_plt.pdf',
       width = 10, height = 5)

< 0

ltz_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', 
                           leglen = -1)
ltz_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/ltz_plt.pdf',
       width = 10, height = 5)

not a number

This raises an error. Test is via testthat

Legloc Options

Top

top_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 'top')
top_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/top_plt.pdf',
       width = 10, height = 5)

Bottom

bot_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 'bottom')
bot_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/bot_plt.pdf',
       width = 10, height = 5)

Right

right_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 'right')
right_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/right_plt.pdf',
       width = 10, height = 5)

Left

left_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 'left')
left_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/left_plt.pdf',
       width = 10, height = 5)

None

none_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 'none')
none_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/none_plt.pdf',
       width = 10, height = 5)

Bad

bad_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', leglen = 10,
                       legloc = 3)
bad_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/bad_plt.pdf',
       width = 10, height = 5)

Colour Vectors

cols = c("#E41A1C","#377EB8","#4DAF4A","#984EA3","#FF7F00","#FFFF33","#A65628",
         "#F781BF")

Named (good)

nmcols = cols
names(nmcols) = c('Other',
                  rev(levels(class_df$Class)[-1]))
nm_gd_plt = plot_tax_bar(class_df, 'Class', colours = nmcols, 
                         sample = 'SampleID')
nm_gd_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/nm_gd_plt.pdf',
       width = 10, height = 5)

Named (bad)

This raises an error. Test is via testthat.

Named (too short)

nmbd_col_plt = plot_tax_bar(class_df, 'Class', colours = nmcols[1:3],
                            sample = 'SampleID')
nmbd_col_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/nmbd_col_plt.pdf',
       width = 10, height = 5)

Unnamed (long enough)

un_col_plt = plot_tax_bar(class_df, 'Class', colours = cols, 
                          sample = 'SampleID')
un_col_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/un_col_plt.pdf',
       width = 10, height = 5)

Unnamed (not long enough)

unbd_col_plt = plot_tax_bar(class_df, 'Class', colours = cols[1:3], 
                          sample = 'SampleID')
unbd_col_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/unbd_col_plt.pdf',
       width = 10, height = 5)

Rotate ticks

rot_plt = plot_tax_bar(fam_df, 'Family', sample = 'SampleID', r_ticks = TRUE)
rot_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/rot_plt.pdf',
       width = 10, height = 5)

Means

Means (good)

mn_plt = plot_tax_bar(fam_df, 'Family', sample = 'Source', means = TRUE)
mn_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/mn_plt.pdf',
       width = 10, height = 5)

Means (good, different ns)

mn_dn_plt = plot_tax_bar(filter(fam_df, SampleID != 'SHCM34'), 'Family',
                         sample = 'Source', means = TRUE)
mn_dn_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/mn_dn_plt.pdf',
       width = 10, height = 5)

Means (forget)

mn_frgt_plt = plot_tax_bar(fam_df, 'Family', sample = 'Source')
mn_frgt_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/mn_frgt_plt.pdf',
       width = 10, height = 5)

Means (forget, different ns)

mn_dn_frgt_plt = plot_tax_bar(filter(fam_df, SampleID != 'SHCM34'), 'Family',
                              sample = 'Source')
mn_dn_frgt_plt
ggsave('~/Projects/Mine/aftersl1p/benchmark/mn_dn_frgt_plt.pdf',
       width = 10, height = 5)

JCSzamosi/aftersl1p documentation built on July 3, 2025, 8:37 p.m.