BMP Data Processing Script
Benjamin Long
2023-10-19
Bush Medicine Processing
Notes before use
Remember to update working directory (wd) and files Must clean all names of Plants for spelling errors (update from the last years file to make things easier) Remember to append the data from 2018 Micro which is in a different format Update microorganism list if needed
Get Librarys
Set WD
Get Data
FloraData <- read.csv("Plant_Sample_Database_2023_Cleaned.csv", TRUE, fileEncoding="UTF-8-BOM")
ChemData <- read.csv("Plant_Extract_Database_2023_Raw.csv", TRUE, fileEncoding="UTF-8-BOM")
MicroData <- read.csv("Antimicrobial_Activity_Database_2023_Raw.csv")
MicroData2018 <- read.csv("Antimicrobial_Activity_Database_2018_Cleaned.csv", TRUE, fileEncoding="UTF-8-BOM")
BacteriaList <- read.csv("MicroorganismList_2023.csv", TRUE, fileEncoding="UTF-8-BOM")
ToxData <- read.csv("Toxicology_Database_2022_Cleaned.csv", fileEncoding="UTF-8-BOM")Generate new Antibacterial Activity dataframe
Micdf2018 <- MicroData2018[,c(1:3)]
Micdf1 <- MicroData[,c(1:3)] %>%
rename(Barcode = Barcode.1, Zone = Zone.1)
Micdf2 <- MicroData[,c(1,5,6)] %>%
rename(Barcode = Barcode.2, Zone = Zone.2)
Micdf3 <- MicroData[,c(1,8,9)] %>%
rename(Barcode = Barcode.3, Zone = Zone.3)
Micdf4 <- MicroData[,c(1,11,12)] %>%
rename(Barcode = Barcode.4, Zone = Zone.4)
Micdf5 <- MicroData[,c(1,14,15)] %>%
rename(Barcode = Barcode.5, Zone = Zone.5)
#Remove all NAs and Zeros from Barcodes
FigData <- rbind(Micdf2018,Micdf1,Micdf2,Micdf3,Micdf4,Micdf5)
FigData["Barcode"][FigData["Barcode"] == 0 ] <- NA
FigData <- na.omit(FigData)
#Rank if Antibacterial
FigData$ABActivity <- c(NA)
Count <- 1
for (val in FigData$Zone) {
if (val != 6) {
if (val != 0) {
FigData[Count,4] <- 1
Count = Count + 1
} else {
FigData[Count,4] <- 0
Count = Count + 1
}
} else {
FigData[Count,4] <- 0
Count = Count + 1
}
}
rm(Count, Micdf1, Micdf2, Micdf3, Micdf4, Micdf5, Micdf2018, val)Clean up of bacteria Names and Assign Gram Stain
Full Microorganism names
Count <- 1
for (val in FigData$Organism) {
if (val %in% BacteriaList$Alt.Name) {
FigData$Organism[Count] <- BacteriaList$Microorganism[match(val, BacteriaList$Alt.Name)]
}
Count <- Count + 1
}
rm(Count, val)Assign Gram
FigData$Gram <- BacteriaList$Gram[match(FigData$Organism, BacteriaList$Microorganism)]Matching of plant names
#Grab Name of Plant and order Dataframe
FigData$GS <- paste(FloraData$Genus[match(FigData$Barcode, FloraData$Barcode)], FloraData$Species.Epithet[match(FigData$Barcode, FloraData$Barcode)], sep = " ")
FigData$Common <- FloraData$Common.Name[match(FigData$Barcode, FloraData$Barcode)]
FigData <- na.omit(FigData)
FigData <- FigData[order(-FigData$ABActivity),]
#Count Times Tested Total each combo
FigData$TestType <- paste(FigData$Organism, FigData$GS, sep = " x ")
TimesTested <- as.data.frame(table(FigData$TestType))
FigData$TimesTested <- TimesTested$Freq[match(FigData$TestType, TimesTested$Var1)]
#Count Times Tested Positive each combo
PosOnlyData <- subset(FigData, ABActivity == 1)
TimesTestedPos <- as.data.frame(table(PosOnlyData$TestType))
FigData$TimesTestedPos <- TimesTestedPos$Freq[match(FigData$TestType, TimesTestedPos$Var1)]
FigData$TimesTestedPos[is.na(FigData$TimesTestedPos)] <- 0
#Tested Ratio
FigData$TestRatio <- paste(FigData$TimesTestedPos, FigData$TimesTested, sep = "/")
#Cleanup of FigData
FigData <- na.omit(FigData)
rownames(FigData) <- c(1:length(rownames(FigData)))
rm(TimesTested, TimesTestedPos, PosOnlyData)Create Heatmap Data
#Create Heatmap Data Frame
HeatmapData <- FigData %>%
select("Organism", "Gram", "ABActivity", "Barcode", "GS", "Common", "TestType", "TestRatio") %>%
distinct(TestType, .keep_all = TRUE) %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4)), NewTest = if_else(Year == max(Year),1,0)) %>%
select(!Year & !Barcode) %>%
arrange(GS)Generate Heatmaps
Note: Some values are in there so that the final combined figure looks good (i.e. legend position)
Normal Heatmap
Plot1 <- ggplot(subset(HeatmapData, Gram == "Gram Positive"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
labs(x = "Flora Scientific Name", y="Gram Positive") +
scale_x_discrete(position = "top", limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 60, vjust = 0.5, hjust=0,face="italic"),
plot.margin=unit(c(0,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
Plot2 <- ggplot(subset(HeatmapData, Gram == "Gram Negative"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
scale_x_discrete(limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
labs(x = "Flora Scientific Name", y="Gram Negative") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
Plot3 <- ggplot(subset(HeatmapData, Gram == "Eukaryote"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
labs(x = "Flora Common Name", y="Eukaryote") +
scale_x_discrete(limit = unique(HeatmapData$GS),
labels = unique(HeatmapData$Common)) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 300, vjust = 0, hjust=0),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="right")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
LegendData <- as.grob(get_legend(Plot3))
HeightList <- unlist(c((40 + 4*count(subset(BacteriaList, Gram == "Gram Positive"))),
(8 + 4*count(subset(BacteriaList, Gram == "Gram Negative"))),
(59 + 4*count(subset(BacteriaList, Gram == "Eukaryote")))))
FinalPlot <- ggarrange(Plot1,
Plot2,
Plot3,
ncol = 1,
nrow = 3,
align ="v",
heights = HeightList,
common.legend = TRUE,
legend="none") %>%
annotate_figure(left = text_grob("Microorgansim", rot = 90, size=12))
FinalPlot <- FinalPlot + annotation_custom(LegendData,
xmin = -0.6, ymin = -0.8)
FinalPlot
ggsave("Antimicrobial_Figure_2023.png",
width=22, height=20, units="cm", dpi = 1000)Heatmap with Tests
Plot1 <- ggplot(subset(HeatmapData, Gram == "Gram Positive"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
geom_text(aes(label = TestRatio), size = 2, color = "grey") +
labs(x = "Flora Scientific Name", y="Gram Positive") +
scale_x_discrete(position = "top", limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 60, vjust = 0.5, hjust=0,face="italic"),
plot.margin=unit(c(0,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
Plot2 <- ggplot(subset(HeatmapData, Gram == "Gram Negative"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
geom_text(aes(label = TestRatio), size = 2, color = "grey") +
scale_x_discrete(limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
labs(x = "Flora Scientific Name", y="Gram Negative") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
Plot3 <- ggplot(subset(HeatmapData, Gram == "Eukaryote"), aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
geom_text(aes(label = TestRatio), size = 2, color = "grey") +
labs(x = "Flora Common Name", y="Eukaryote") +
scale_x_discrete(limit = unique(HeatmapData$GS),
labels = unique(HeatmapData$Common)) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 300, vjust = 0, hjust=0),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="right")+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
LegendData <- as.grob(get_legend(Plot3))
HeightList <- unlist(c((40 + 4*count(subset(BacteriaList, Gram == "Gram Positive"))),
(8 + 4*count(subset(BacteriaList, Gram == "Gram Negative"))),
(59 + 4*count(subset(BacteriaList, Gram == "Eukaryote")))))
FinalPlot <- ggarrange(Plot1,
Plot2,
Plot3,
ncol = 1,
nrow = 3,
align ="v",
heights = HeightList,
common.legend = TRUE,
legend="none") %>%
annotate_figure(left = text_grob("Microorgansim", rot = 90, size=12))
FinalPlot <- FinalPlot + annotation_custom(LegendData,
xmin = -0.6, ymin = -0.8)
FinalPlot
ggsave("Antimicrobial_Figure_2023_Frequency.png",
width=22, height=20, units="cm", dpi = 1000)Heatmap that hightlights new tests
PlotLegendOnly <- ggplot(HeatmapData, aes(GS, Organism, fill = ABActivity)) +
geom_tile() +
scale_fill_gradient(na.value = NA,
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
Plot1 <- ggplot(subset(HeatmapData, Gram == "Gram Positive"), aes(GS, Organism)) +
geom_tile(aes(fill = ABActivity), alpha = 0.2) +
geom_tile(aes(fill = ifelse(NewTest == 1, ABActivity, NA), color = ifelse(NewTest == 1, NewTest, NA)), size=0.8) +
labs(x = "Flora Scientific Name", y="Gram Positive") +
scale_x_discrete(position = "top", limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 60, vjust = 0.5, hjust=0,face="italic"),
plot.margin=unit(c(0,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_gradient(aesthetics = "fill",
na.value = NA,
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)+
scale_fill_gradient(aesthetics = "color",
low = "white",
high = "white",
na.value = NA,
breaks = c(0, 1)
)## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Plot2 <- ggplot(subset(HeatmapData, Gram == "Gram Negative"), aes(GS, Organism, fill = NewTest), colour = "white") +
geom_tile(aes(fill = ABActivity), alpha = 0.2) +
geom_tile(aes(fill = ifelse(NewTest == 1, ABActivity, NA), color = ifelse(NewTest == 1, NewTest, NA)), size=0.8) +
scale_x_discrete(limits = unique(HeatmapData$GS), drop = FALSE) +
scale_y_discrete(limits=rev) +
labs(x = "Flora Scientific Name", y="Gram Negative") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="none")+
scale_fill_gradient(na.value = "#FFFFFF00",
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)+
scale_fill_gradient(aesthetics = "color",
low = "white",
high = "white",
na.value = NA,
breaks = c(0, 1)
)
Plot3 <- ggplot(subset(HeatmapData, Gram == "Eukaryote"), aes(GS, Organism, fill = NewTest), colour = "white") +
geom_tile(aes(fill = ABActivity), alpha = 0.2) +
# geom_tile(aes(fill = ifelse(NewTest == 1, ABActivity, NA), color = ifelse(NewTest == 1, NewTest, NA)), size=0.8) +
labs(x = "Flora Common Name", y="Eukaryote") +
scale_x_discrete(limit = unique(HeatmapData$GS),
labels = unique(HeatmapData$Common)) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 300, vjust = 0, hjust=0),
plot.margin=unit(c(0.5,2,0.5,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"),
legend.position="right")+
scale_fill_gradient(na.value = "#FFFFFF00",
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)+
scale_fill_gradient(aesthetics = "color",
low = "white",
high = "white",
na.value = NA,
breaks = c(0, 1)
)
LegendData <- as.grob(get_legend(PlotLegendOnly))
HeightList <- unlist(c((40 + 4*count(subset(BacteriaList, Gram == "Gram Positive"))),
(8 + 4*count(subset(BacteriaList, Gram == "Gram Negative"))),
(59 + 4*count(subset(BacteriaList, Gram == "Eukaryote")))))
FinalPlot <- ggarrange(Plot1,
Plot2,
Plot3,
ncol = 1,
nrow = 3,
align ="v",
heights = HeightList,
common.legend = TRUE,
legend="none") %>%
annotate_figure(left = text_grob("Microorgansim", rot = 90, size=12))
FinalPlot <- FinalPlot + annotation_custom(LegendData,
xmin = -0.6, ymin = -0.8)
FinalPlot
ggsave("Antimicrobial_Figure_2023_NewTestHighlight.png",
width=22, height=20, units="cm", dpi = 1000)Heatmap for each Barcode
FigData_Barcode <- FigData %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4)), Barcode = paste0("BMP", Barcode)) %>%
arrange(Year)
Plot1 <- FigData_Barcode %>%
filter(Gram == "Gram Positive") %>%
ggplot(aes(reorder(Barcode, Year), Organism, fill = ABActivity)) +
geom_tile() +
labs(x = "Barcodes", y="Gram Positive") +
scale_x_discrete(position = "top", limits = unique(FigData_Barcode$Barcode), drop = FALSE) +
scale_y_discrete(limits=rev) +
theme(axis.text.x = element_text(angle = 60, vjust = 0.5, hjust=0,face="italic"),
legend.position="none",
plot.margin=unit(c(0,1,1,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"))
Plot2 <- FigData_Barcode %>%
filter(Gram == "Gram Negative") %>%
ggplot(aes(reorder(Barcode, Year), Organism, fill = ABActivity)) +
geom_tile() +
scale_x_discrete(limits = unique(FigData_Barcode$Barcode), drop = FALSE) +
scale_y_discrete(limits=rev) +
labs(y="Gram Negative") +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
legend.position="none",
plot.margin=unit(c(0,1,1,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"))
Plot3 <- FigData_Barcode %>%
filter(Gram == "Eukaryote") %>%
ggplot(aes(reorder(Barcode, Year), Organism, fill = ABActivity)) +
geom_tile() +
labs(y="Eukaryote") +
scale_x_discrete(limit = unique(FigData_Barcode$Barcode)) +
scale_y_discrete(limits=rev) +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
legend.position="bottom",
plot.margin=unit(c(0,1,1,1), "cm"),
axis.title.y=element_text(size=10,face="bold"),
axis.text.y=element_text(face="italic"))+
scale_fill_continuous(
breaks = c(0, 1),
labels = c("No Activity", "Activity"),
guide = guide_legend(
title = "Antimicrobial Activity",
title.position = "top",
label.hjust = 0,
label.vjust = 0.5)
)
HeightList <- unlist(c((40 + 4*count(subset(BacteriaList, Gram == "Gram Positive"))),
(11 + 4*count(subset(BacteriaList, Gram == "Gram Negative"))),
(33 + 4*count(subset(BacteriaList, Gram == "Eukaryote")))))
FinalPlot <- ggarrange(Plot1, Plot2, Plot3,
ncol = 1,
nrow = 3,
align ="v",
heights = HeightList) %>%
annotate_figure(left = text_grob("Microorgansim", rot = 90, size=12))
FinalPlot
ggsave("Antimicrobial_Figure_2023_Barcode.png",
width=30, height=20, units="cm", dpi = 1000)df1 <- FloraData %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4))) %>%
group_by(Year) %>%
summarise(Number = n(), Sample = "Flora Sample")
df2 <- ChemData %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4))) %>%
group_by(Year) %>%
summarise(Number = n(), Sample = "Chemical Extract")
df3 <- FigData %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4))) %>%
group_by(Year) %>%
summarise(Number = n(), Sample = "Antimicrobial Assay")
df4 <- ToxData %>%
mutate(Year = as.numeric(substr(Barcode, 1, 4))) %>%
group_by(Year) %>%
summarise(Number = n(), Sample = "Toxicity Assay")
Generic_Stats <- rbind(df1,df2,df3,df4)
rm(df1, df2, df3, df4)
Generic_Stats <- Generic_Stats %>%
mutate_at("Year", ~na_if(., 0)) %>%
na.omit()
Generic_Stat_Plot <- Generic_Stats %>%
mutate(Sample = factor(Sample,
levels=c("Flora Sample",
"Chemical Extract",
"Antimicrobial Assay",
"Toxicity Assay"))) %>%
group_by(Sample) %>%
arrange(Year) %>%
mutate(Cum = cumsum(Number),
MAX.Year = if_else(Year == max(Year), Year, NA),
MAX.Cum = if_else(Cum == max(Cum), Cum, NA)) %>%
ggplot()+
geom_bar(aes(x=Year, y=Number, fill = Sample), stat="identity", colour = "black", width=0.8)+
geom_line(aes(x=Year, y=Cum, colour = Sample))+
geom_point(aes(x=MAX.Year, y=MAX.Cum, colour = Sample))+
geom_text(aes(x=MAX.Year, y=MAX.Cum, label = MAX.Cum),
hjust = "inward",
nudge_x = -0.1,
nudge_y = 30)+
labs(y= "Number of samples Processed")+
theme(legend.position = "bottom",
legend.title=element_blank())+
ggtitle("Number of Samples Processed and Analysed to Data", subtitle = "Lines cumulative ")+
facet_wrap(~ Sample, nrow = 1)
Generic_Stat_Plot## Warning: Removed 13 rows containing missing values (`geom_point()`).## Warning: Removed 13 rows containing missing values (`geom_text()`).
ggsave("Total_Sample_Number_2023.png",
width=20, height=10, units="cm", dpi = 1000)## Warning: Removed 13 rows containing missing values (`geom_point()`).
## Removed 13 rows containing missing values (`geom_text()`).Export Processed Dataframe
#Export Dataframe
write.csv(HeatmapData, "HeatMap_Processed_Data_Export.csv", row.names=FALSE)