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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| rm(list = ls()) | ||
| library(reshape2) | ||
| library(ggplot2) | ||
|
|
||
| threshold <- 0.01 | ||
| profile <- read.csv('animal_guts_profile.tsv', sep='\t') | ||
| profile <- profile[grepl("s__|sgb_|UNKNOWN", profile$Taxonomy) & | ||
| !grepl("t__", profile$Taxonomy),] | ||
| profile[,-1][profile[,-1] < threshold] <- 0 | ||
| profile[profile$Taxonomy == "UNKNOWN",-1] = profile[profile$Taxonomy == "UNKNOWN",-1] + | ||
| (100 - colSums(profile[,-1])) | ||
|
|
||
| # Plot an ECDF of unknown percentage by sample | ||
| unknownECDF <- function(profile) { | ||
| df <- data.frame("abundance" = c(unlist(profile[profile$Taxonomy == "UNKNOWN",-1]), | ||
| colSums(profile[grepl("s__", profile$Taxonomy),-1]), | ||
| colSums(profile[grepl("sgb_", profile$Taxonomy),-1])), | ||
| "type" = c(rep("Unknown", ncol(profile) - 1), | ||
| rep("Known", ncol(profile) - 1), | ||
| rep("SGB", ncol(profile) - 1)), | ||
| "sample" = rep(colnames(profile)[-1], 3)) | ||
|
|
||
| df$sample <- factor(df$sample, levels = df$sample[df$type == "Unknown"][order(df$abundance[df$type == "Unknown"])]) | ||
|
|
||
| p1 <- ggplot(df, aes(fill=type, y=abundance, x = sample)) + | ||
| geom_bar(position="fill", stat="identity") + | ||
| theme(axis.text.x=element_blank()) + | ||
| ylab("Abundance") + xlab("Sample") + | ||
| labs(fill = "Abundance type") | ||
|
|
||
| dir.create(file.path("figures/"), showWarnings = FALSE) | ||
| ggsave("figures/ECDF.png", p1, width=18, height=10, units = 'cm', dpi=1000) | ||
| } | ||
|
|
||
| unknownECDF(profile) |
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| "sample_id" "diet" "flight" "habitat" "class" | ||
| "ERR5005154" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005155" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005158" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005160" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005161" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005164" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005165" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005166" "Omnivore" "Non-flying land animal" "Farm" "Aves" | ||
| "ERR5005167" "Herbivore" "Non-flying land animal" "Farm" "Mammalia" | ||
| "ERR5005168" "Omnivore" "Non-flying land animal" "Farm" "Aves" | ||
| "ERR5005169" "Omnivore" "Non-flying land animal" "Farm" "Aves" | ||
| "ERR5005170" "Omnivore" "Non-flying land animal" "Farm" "Mammalia" | ||
| "ERR5005284" "Herbivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005285" "Herbivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005286" "Insectivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005287" "Omnivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005289" "Herbivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005302" "Carnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005305" "Herbivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005309" "Carnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005310" "Omnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005311" "Insectivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005312" "Carnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005314" "Omnivore" "Non-flying land animal" "Captive herp" "Amphibia" | ||
| "ERR5005315" "Insectivore" "Non-flying land animal" "Captive herp" "Amphibia" | ||
| "ERR5005317" "Omnivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005318" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005319" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005320" "Omnivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005321" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005322" "Herbivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005325" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005326" "Carnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005330" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005335" "Herbivore" "Non-flying land animal" "Captive aquatic mammal" "Mammalia" | ||
| "ERR5005162" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005334" "Herbivore" "Non-flying land animal" "Captive aquatic mammal" "Mammalia" | ||
| "ERR5005156" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005157" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005159" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005163" "Carnivore" "Marine animal" "Ocean" "Mammalia" | ||
| "ERR5005171" "Herbivore" "Flying land animal" "Farm" "Aves" | ||
| "ERR5005283" "Carnivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005288" "Omnivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005290" "Insectivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005291" "Carnivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005292" "Insectivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005293" "Carnivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005301" "Insectivore" "Non-flying land animal" "Captive terrestrial mammal" "Mammalia" | ||
| "ERR5005303" "Herbivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005304" "Omnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005306" "Carnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005307" "Herbivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005308" "Carnivore" "Non-flying land animal" "Captive herp" "Reptilia" | ||
| "ERR5005313" "Omnivore" "Non-flying land animal" "Captive herp" "Amphibia" | ||
| "ERR5005316" "Insectivore" "Non-flying land animal" "Captive herp" "Amphibia" | ||
| "ERR5005323" "Omnivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005324" "Omnivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005327" "Carnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005328" "Omnivore" "Flying land animal" "Captive bird" "Aves" | ||
| "ERR5005329" "Omnivore" "Non-flying land animal" "Captive bird" "Aves" | ||
| "ERR5005331" "Herbivore" "Non-flying land animal" "Captive bird" "Aves" |
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