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barplot_16S_taxa.R
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setwd("U:/")
library(RColorBrewer)
library(ggplot2)
genusPalette <- c( Acinetobacter="#CDCD00",
Actinomyces="#BDB76B",
Anaerococcus="#CDCDC1",
Bacteroides="#FF8C69",
#Bifidobacterium="#000080",
Bifidobacterium="gold",
Bilophila="#EED5D2",
Candida="#CDC9C9",
#Citrobacter="#FFA500",
Citrobacter="blue4",
#Clostridium="#848484",
Clostridium="red1",
Coprobacter="#FFE4E1",
Coprobacillus="#EED5D2",
Corynebacterium="#FFFAF0",
Dermabacter="#EEEEE0",
#Enterococcus="#76EE00",
Enterococcus="lightskyblue",
Escherichia="#FFFF00",
Eggerthella="#E0EEE0",
Enterobacter="#FF7F00",
Finegoldia="#FFDAB9",
Flavonifractor="#F5F5DC",
Gemella="#EECBAD",
Granulicatella="#E3E3E3",
Haemophilus="#00FA9A",
#Klebsiella="#FFBBFF",
Klebsiella="navy",
Lactobacillus="#DB7093",
Parabacteroides="#bc4512",
Peptoniphilus="#9B30FF",
Peptostreptococcaceae="#912CEE",
Prevotella="#2e9f97",
Propionibacterium="#00C5CD",
Proteus="#FAFAD2",
Pseudomonas="#BCD2EE",
Raoultella="#9268a5",
Rothia="#00EEEE",
Serratia="#BDB76B",
Shigella="#D2B48C",
#Streptococcus="#DAA520",
Streptococcus="rosybrown1",
Staphylococcus="royalblue1",
Stenotrophomonas="#627037",
Ureaplasma="#EEE0E5",
Staphylococcus="#FF4040",
Varibaculum="#a5571c",
Veillonella="#F4A460",
Bradyrhizobium="black",
Burkholderia="brown",
Neisseria="#FF00FF",
Ochrobactrum="#848484",
Peptostreptococcus="#282828",
Roseomonas="#B7B7B7"
)
speciesPalette <- c(Acinetobacter_johnsonii="#CDCD00",
Acinetobacter_junii="#8B8B00",
Actinomyces_neuii="#BDB76B",
Acinetobacter_unclassified="#808000",
Actinomyces_urogenitalis="#d88c49",
Anaerococcus_prevotii="#CDCDC1",
Bacteroides_fragilis="#FF8C69",
Bacteroides_ovatus="#EE8262",
Bacteroides_uniformis="#CD7054",
Bacteroides_vulgatus="#FF7256",
Bifidobacterium_bifidum ="#0000FF",
Bifidobacterium_breve="#000080",
Bifidobacterium_animalis="#27408B",
Bifidobacterium_longum="#6495ED",
Bifidobacterium_dentium="#104E8B",
Bilophila_wadsworthia="#EED5D2",
Bilophila_unclassified="#FFE4E1",
Candida_albicans="#CDC9C9",
Citrobacter_freundii="#FFA500",
Citrobacter_unclassified="#FF9912",
Citrobacter_koseri="#FFD700",
Clostridium_difficile="#848484",
Clostridium_perfringens="#1E1E1E",
Clostridium_ramosum="#555555",
Clostridium_symbiosum="#515151",
Clostridium_bartlettii="#5B5B5B",
Clostridium_glycolicum="#AAAAAA",
Coprobacter_fastidiosus="#FFE4E1",
Coprobacillus_unclassified="#EED5D2",
Corynebacterium_accolens="#FFFAF0",
Corynebacterium_amycolatum="#F5DEB3",
Corynebacterium_bovis="#FFE7BA",
Corynebacterium_kroppenstedtii="#EED8AE",
Corynebacterium_striatum="#CDBA96",
Corynebacterium_tuberculostearicum="#FDF5E6",
Corynebacterium_pseudogenitalium="#FFFAF0",
Dermabacter_sp_HFH0086="#EEEEE0",
Enterococcus_faecalis="#76EE00",
Enterococcus_faecium="#66CD00",
Enterococcus_avium="#6E8B3D",
Escherichia_coli="#FFFF00",
Escherichia_unclassified="#EEEE00",
Eggerthella_lenta="#E0EEE0",
Eggerthella_unclassified="#C1CDC1",
Enterobacter_aerogenes="#FF7F00",
Enterobacter_cloacae="#EE7600",
Enterobacter_hormaechei="#CD6600",
Finegoldia_magna="#FFDAB9",
Flavonifractor_plautii="#F5F5DC",
Gemella_haemolysans="#EECBAD",
Gemella_unclassified="#CDAF95",
Granulicatella_unclassified="#E3E3E3",
Granulicatella_adiacens="#E0E0E0",
Haemophilus_parainfluenzae="#00FA9A",
Klebsiella_oxytoca="#FFBBFF",
Klebsiella_pneumoniae="#CD96CD",
Klebsiella_unclassified="#DDA0DD",
Lactobacillus_acidophilus="#DB7093",
Lactobacillus_crispatus="#FF82AB",
Lactobacillus_fermentum="#CD6889",
Lactobacillus_rhamnosus="#FFB6C1",
Lactobacillus_gasseri="#FFC0CB",
Lactobacillus_animalis="#FF3E96",
Lactobacillus_casei_paracasei="#EE3A8C",
Lactobacillus_plantarum="#8B2252",
Parabacteroides_distasonis="#bc4512",
Parabacteroides_unclassified="brown",
Peptoniphilus_rhinitidis="#9B30FF",
Peptostreptococcaceae_noname_unclassified="#912CEE",
Prevotella_bivia="#2e9f97",
Propionibacterium_acnes="#00C5CD",
Propionibacterium_avidum="#00868B",
Propionibacterium_granulosum="#00F5FF",
Propionibacterium_sp_HGH0353="#00868B",
Proteus_mirabilis="#FAFAD2",
Pseudomonas_unclassified="#BCD2EE",
Pseudomonas_aeruginosa="#CAE1FF",
Raoultella_ornithinolytica="#9268a5",
Rothia_mucilaginosa="#00EEEE",
Serratia_marcescens="#BDB76B",
Shigella_sonnei="#D2B48C",
Streptococcus_agalactiae="#DAA520",
Streptococcus_anginosus="#FFC125",
Streptococcus_constellatus="#EEB422",
Streptococcus_gallolyticus="#FF4500",
Streptococcus_gordonii="#CD950C",
Streptococcus_mitis_oralis_pneumoniae="#CD9B1D",
Streptococcus_parasanguinis="#B8860B",
Streptococcus_phage_Cp_1="#EEAD0E",
Streptococcus_salivarius="#8B6508",
Streptococcus_sp_C150="#CD950C",
Streptococcus_thermophilus="#FFB90F",
Streptococcus_urinalis="#EE9A00",
Streptococcus_vestibularis="#89661c",
Stenotrophomonas_maltophilia="#627037",
Stenotrophomonas_unclassified="#BDFCC9",
Stenotrophomonas_maltophilia="#32CD32",
Ureaplasma_parvum="#EEE0E5",
Staphylococcus_epidermidis="#FF4040",
Staphylococcus_haemolyticus="#EE3B3B",
Staphylococcus_hominis="#8B2323",
Staphylococcus_lugdunensis="#B22222",
Staphylococcus_phage_ROSA="#CD2626",
Staphylococcus_warneri="#EE2C2C",
Staphylococcus_aureus="#FF0000",
Staphylococcus_caprae_capitis="#DC143C",
Varibaculum_cambriense="#a5571c",
Veillonella_atypica="#F4A460",
Veillonella_parvula="#8B4513",
Veillonella_unclassified="#d88c49",
Veillonella_sp_oral_taxon_780="#9b6336",
Veillonella_dispar="#da8d73",
"#cc6949")
familyPalette <-c(
Bacteroidaceae="#CDCD00",
Porphyromonadaceae="#BDB76B",
Tannerellaceae="#CDCDC1",
Rhizobiaceae="#FF8C69",
Enterobacteriaceae="#EECBAD",
Pasteurellaceae="#EED5D2",
Moraxellaceae="#CDC9C9",
Xanthomonadaceae="#FFA500",
Actinomycetaceae="#848484",
Bifidobacteriaceae="#000080",
Corynebacteriaceae="#FFFF00",
Dermabacteraceae="#E0EEE0",
Nocardioidaceae="#F5F5DC",
Propionibacteriaceae="#00C5CD",
Bacillaceae="#2e9f97",
Staphylococcaceae="#9268a5",
Enterococcaceae="#DAA520",
Lactobacillaceae="#a5571c",
Streptococcaceae="#FF4040",
Clostridiaceae="#EEE0E5",
Lachnospiraceae="#00FA9A",
Peptostreptococcaceae="#FAFAD2",
Ruminococcaceae="#F4A460"
)
#provide the filename below
Stack_data <- read.csv("Q088.csv")
#Stack_data_2 <- as.character(Stack_data$ID)
#head(Stack_data_2)
head(Stack_data)
png("Q088_data.png",
width = 8*500, # 5 x 300 pixels
height = 10*500,
res = 600, # 300 pixels per inch
pointsize = 8)
library(reshape2)
df_long <- melt(Stack_data, id.vars ="ID" , variable.name ="Species")
head(df_long)
library(scales)
ncol(Stack_data)
library(ggplot2)
n <- 60
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
color_new = grDevices::colors()[grep('gr(a|e)y', grDevices::colors(), invert = T)]
#ggplot(df_long, aes(x = ID, y = value, fill =Species)) +
# geom_bar(stat ="identity" , position = position_fill())+ theme(legend.position="right" , legend.direction="horizontal" , legend.title = element_blank())+
# labs(x="" , y="EGGNOG categories %")+theme(axis.text.x=element_text(angle=90, hjust=1, vjust=0.5)) + scale_fill_manual(values =familyPalette )
ggplot(df_long[order(df_long$value, decreasing = F),], aes(x = ID, y = value, fill =Species ,drop=TRUE )) +
geom_bar(stat ="identity" , position = position_fill()) + theme(legend.text = element_text(size=10,face= "italic"),legend.position="right" , legend.direction="vertical" , legend.title = element_blank())+
labs(x=" " , y=" ") +theme(axis.text.x=element_text(angle=90, size =20, colour="black"),
axis.title.y = element_text(angle=90, hjust=1, vjust=1, size=20),
axis.text.y = element_text(size=20,colour = "black"),
axis.title.x = element_text(size=25)) + scale_fill_manual(values = genusPalette)
dev.off()