load packages

require(ggplot2)
## Loading required package: ggplot2
require(stringr)
## Loading required package: stringr
require(plyr)
## Loading required package: plyr
suppressPackageStartupMessages(require(dplyr))

Plot code

## plot without Will be resequenced.

Will_be_resequenced <- read.delim("~/Projects/impute_to_Sequence/Sequencing_96_samples/Will_be_resequenced.txt",
                                             header=FALSE, stringsAsFactors=FALSE)

x <- read.table("~tikn/Projects/impute_to_Sequence/Sequencing_96_samples/all_samples_with_frag_count_without_will_be_resequenced.txt",
                     stringsAsFactors = F, sep = "\t") %>% tbl_df()
x$V2 <- as.integer(str_replace_all(x$V2, pattern = ",", "")) ## remove , from file.
x2 <- arrange(x, V1)
x3 <- mutate(x2, bases = V2 * 125)
x3$Sample <- as.integer(stringr::str_extract(x3$V1, "^[0-9]{1,2}")) # pull out Sample number to column Sample

df1 <- mutate(x3, lane = str_extract(V1, "L[\\d]{3}"), 
                  read = str_extract(V1, "R[12]{1}")) %>% 
    filter(read == "R1") %>% 
    mutate(yield = bases*2)

to_show <- seq(1,96)
to_plot <- split(to_show, ceiling(seq_along(to_show)/16))
names(to_plot) <- paste("Part", seq(1,6,1), sep = "")

yield_plot <- function(x) {
    ggplot(data = filter(df1, Sample %in% x), aes(factor(Sample), yield/1e9, fill = lane)) + 
    geom_bar(stat = "identity", position = "dodge") + 
    theme_light() + 
    scale_fill_brewer(type="qual") + 
#   facet_wrap(~project, nrow = 2) + 
    xlab("Sample") + ylab("billion reads")
}

llply(to_plot, yield_plot)
## $Part1

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## $Part2

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## $Part3

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## $Part4

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## $Part5

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## $Part6