Plot the result of a mt test phyloseq::mt()

Usage

plot_mt(mt = NULL, alpha = 0.05, color_tax = "Class", taxa = "Species")

Arguments

mt

(required) Result of a mt test from the function phyloseq::mt().

alpha

(default: 0.05) Choose the cut off p-value to plot taxa.

color_tax

(default: "Class") A taxonomic level to color the points.

taxa

(default: "Species") The taxonomic level you choose for x-positioning.

Value

a ggplot2 plot of result of a mt test

See also

phyloseq::mt()

Author

Adrien Taudière

Examples

# \donttest{
# Filter samples that don't have Time
data_fungi_mini2 <- subset_samples(data_fungi_mini, !is.na(Time))
res <- mt(data_fungi_mini2, "Time", method = "fdr", test = "f", B = 300)
#> B=300
#> b=3	b=6	b=9	b=12	b=15	b=18	b=21	b=24	b=27	b=30	
#> b=33	b=36	b=39	b=42	b=45	b=48	b=51	b=54	b=57	b=60	
#> b=63	b=66	b=69	b=72	b=75	b=78	b=81	b=84	b=87	b=90	
#> b=93	b=96	b=99	b=102	b=105	b=108	b=111	b=114	b=117	b=120	
#> b=123	b=126	b=129	b=132	b=135	b=138	b=141	b=144	b=147	b=150	
#> b=153	b=156	b=159	b=162	b=165	b=168	b=171	b=174	b=177	b=180	
#> b=183	b=186	b=189	b=192	b=195	b=198	b=201	b=204	b=207	b=210	
#> b=213	b=216	b=219	b=222	b=225	b=228	b=231	b=234	b=237	b=240	
#> b=243	b=246	b=249	b=252	b=255	b=258	b=261	b=264	b=267	b=270	
#> b=273	b=276	b=279	b=282	b=285	b=288	b=291	b=294	b=297	b=300	
#> r=1	r=2	r=3	r=4	r=5	r=6	r=7	r=8	r=9	r=10	
#> r=11	r=12	r=13	r=14	r=15	r=16	r=17	r=18	r=19	r=20	
#> r=21	r=22	r=23	r=24	r=25	r=26	r=27	r=28	r=29	r=30	
#> r=31	r=32	r=33	r=34	r=35	r=36	r=37	r=38	r=39	r=40	
#> r=41	r=42	r=43	r=44	r=45	
plot_mt(res)
#> Warning: invalid factor level, NA generated

plot_mt(res, taxa = "Genus", color_tax = "Order")
#> Warning: invalid factor level, NA generated

# }