# R/compare_te.R In DambrosiCode/TEGrapher: What the Package Does (One Line, Title Case)

#### Defines functions compare

```#' Generates graph with moving average of TE insertion frequency and count
#' @param data Data sheet
#' @param pop Population from which to build graph
#' @param chrom Chromosome from population
#' @param gene (Optional) Gene or genes to mark on graph with vertical line
#' @param mean.window Size of window averaging frequency
#' @param total.window Size of window averaging TE count
#' @mean.fit (Default 0.2) Fit of Loewess curve for frequency
#' @total.fit (Default 0.2) Fit of Loewess curve for count
#' @export
#' @example
#' compare(data = te, pop = CH2012, chr = "chrIV", gene = 12e6, mean.window = 30000, total.window = 30000, mean.fit = 0.2, total.fit = 0.2)

compare <- function(data, pop, chrom, gene, mean.window, total.window, mean.fit = .2, total.fit = .2){
if (!requireNamespace("ggplot2", quietly = TRUE))
install.packages("ggplot2")
library(ggplot2)

#get chromosome
chr <- data[which(data\$Chr == chrom),]

#get frequency and totals vectors
if (is.na(gene)) {
rs.freq <- mean.te(mean.window, chr, pop)
} else{
rs.freq <- mean.te(mean.window, chr, pop, gene)
}
#get data for graph
sum.max <- rs.totals[which.max(rs.totals[,2]),2]

y2 <- rs.totals[,2] / sum.max
x2 <- rs.totals[,1]

y1 <- rs.freq[,2]
x1 <- rs.freq[,1]

#make sure data frames are equal
for (i in (length(rs.freq[,1])-1):length(rs.totals[,1])+1) {
x2[i] <- NA
y2[i] <- NA
}
df <- data.frame(x1, y1, x2, y2)

#plot
c <- ggplot(df, aes(x1, y = value, color = Legend)) +
geom_point(aes(y = y2, x = x2, col = "Total"), size = 1) +
geom_point(aes(y = y1, x = x1, col = "Freq"), size = 1) +
geom_smooth(span = total.fit, aes(y = y2, x = x2, col = "Total Fit"), size = 1, se = F) +
geom_smooth(span = mean.fit, aes(y = y1, x = x1, col = "Freq Fit"), size = 1, se = F) +
scale_color_manual(values = c('purple', 'blue', 'orange', 'red')) +
geom_vline(aes(xintercept = gene+span)) +
xlab("Physical Position") + ylab("Freq") + ggtitle(paste(chrom, "of Pop", pop)) +
scale_y_continuous(sec.axis = sec_axis(~.*sum.max, name = "Count"))

#debug

#plot
return(c)
}
```
DambrosiCode/TEGrapher documentation built on Nov. 20, 2019, 6:29 a.m.