Fred wants about 10 clones to check expression with for his in-situ sequencing/expression analysis.
require(reshape2)
## Loading required package: reshape2
require(plotrix)
## Loading required package: plotrix
require(grid)
## Loading required package: grid
require(plyr)
## Loading required package: plyr
require(ggplot2)
## Loading required package: ggplot2
require(car)
## Loading required package: car
## Loading required package: MASS
## Loading required package: nnet
require(xtable)
## Loading required package: xtable
#
# -----------------------------------------------------------------------------
# RUN-ALL - set up the environment
dropbox_dir <- "/Users/dbgoodman/Dropbox/ecre/ngs/"
# dropbox_dir <- '/home/dbg/Dropbox/ecre/ngs/'
pdf_dir <- paste(dropbox_dir, "plots/2012.10.01/", sep = "")
csv_dir <- paste(dropbox_dir, "rdata/", sep = "")
load(file = paste(pdf_dir, "data_final.Rdata", sep = ""))
Here is a plot of all clones.
ggplot(subset(ngs.flow.avg, !concat & subset.min2), aes(x = prot, y = prot.flow,
label = well, ymin = prot.flow.min, ymax = prot.flow.max)) + geom_text(size = 4) +
geom_errorbar() + scale_x_log10(breaks = logbreaks, name = "log10(Protein Level HiSeq)") +
scale_y_log10(breaks = logbreaks, name = "log10(Protein Level Flow)") +
theme_bw()
## Warning: Removed 7 rows containing missing values (geom_text).
Let's pick 12 in a range and show only those:
1-H02
2-B07
1-H07
2-A11
2-G01
2-D02
2-F12
2-D11
2-D07
1-C12
2-E12
1-A11
chosen_wells = c("1-H02", "2-B07", "1-H07", "2-A11", "2-G01", "2-D02", "2-F12",
"2-D11", "2-D07", "1-C12", "2-E12", "1-A11")
ggplot(subset(ngs.flow.avg, !concat & subset.min2 & well %in% chosen_wells),
aes(x = prot, y = prot.flow, label = well, ymin = prot.flow.min, ymax = prot.flow.max)) +
geom_text(size = 4) + geom_errorbar() + scale_x_log10(breaks = logbreaks,
name = "log10(Protein Level HiSeq)") + scale_y_log10(breaks = logbreaks,
name = "log10(Protein Level Flow)") + theme_bw()
Print out the corresponding promo/rbs combinations for these wells and their DNA sequences:
chosen_sequences <- subset(ngs.flow, paste(plate, well, sep = "-") %in% chosen_wells)[,
c("plate", "well", "target")]
chosen_sequences = chosen_sequences[!duplicated(chosen_sequences), ]
chosen_targets <- unique(chosen_sequences$target)
print(xtable(chosen_sequences), type = "html", include.rownames = F)
| plate | well | target |
|---|---|---|
| 1 | H02 | BBa_J23117–apFAB832 |
| 2 | B07 | BBa_J23116–salis-1-1 |
| 1 | H07 | BBa_J23106–apFAB927 |
| 2 | G01 | apFAB55–apFAB895 |
| 2 | A11 | apFAB300–salis-4-4 |
| 2 | D02 | apFAB67–apFAB864 |
| 2 | D11 | apFAB322–Anderson_RBS |
| 2 | F12 | apFAB130–apFAB857 |
| 1 | A11 | apFAB346–B0030_RBS |
| 2 | D07 | apFAB321–apFAB820 |
| 2 | E12 | apFAB339–apFAB904 |
| 1 | C12 | apFAB72–apFAB889 |
Here are the corresponding sequences:
fasta_file = paste("/Users/dbgoodman/Dropbox/ecre/library clonings", "/manual_48_realign/202.norestrict.fa",
sep = "")
write.table(chosen_targets, file = paste(pdf_dir, "chosen_seqs.txt", sep = ""),
sep = ",", row.names = F, col.names = F, quote = F)
fasta_file = paste(csv_dir, "202.norestrict.fa", sep = "")
intern = system(paste("grep -A1 -F -f", paste(pdf_dir, "chosen_seqs.txt", sep = ""),
fasta_file), intern = T)
print(noquote(intern))
## [1] >apFAB55--apFAB895
## [2] TTGACATAAAGTCTAACCTATAGGTATAATGTGTGGATCTGGCatcttaatctagctagggacctttt
## [3] --
## [4] >apFAB72--apFAB889
## [5] TTGACATCGCATCTTTTTGTACCCATAATTATTTCATGCGTCatcttaatctagcggaggaggattt
## [6] --
## [7] >apFAB67--apFAB864
## [8] TTGACATCAGGAAAATTTTTCTGCATAATTATTTCATATCACatcttaatctagcccgggagcattt
## [9] --
## [10] >apFAB339--apFAB904
## [11] TTGACAATTAATCATCCGGCTCGTAATTTATGTGGATAGGAatcttaatctagcgggggatttttt
## [12] --
## [13] >apFAB321--apFAB820
## [14] TTGACAATTAATCATCCGGCTCGTAACTTATGTGGACTCGGatcttaatctagctgcggagggttt
## [15] --
## [16] >apFAB322--Anderson_RBS
## [17] TTGCGTATTAATCATCCGGCTCGTATAATGTGTGGATGATCtctagagaaagaggggacaaact
## [18] --
## [19] >apFAB346--B0030_RBS
## [20] TTGACAATTAATCATCCGGCTCGTAATGTTTGTGGATAGCTattaaagaggagaaatta
## [21] --
## [22] >apFAB300--salis-4-4
## [23] TTGCCGCTTAATCATCCGGCTCGTATAATGTGTGGATCTTCaatctcttatatcaaatataaggaggat
## [24] --
## [25] >apFAB130--apFAB857
## [26] CACGGTGTTAGACATAAAGTCTAACCTATAGGTATAATGTGTGGATCCGTGatcttaatctagctgaggaaagttt
## [27] --
## [28] >BBa_J23106--apFAB927
## [29] TTTACGGCTAGCTCAGTCCTAGGTATAGTGCTAGCGATAGatcttaatctagctggggactgttt
## [30] --
## [31] >BBa_J23116--salis-1-1
## [32] TTGACAGCTAGCTCAGTCCTAGGGACTATGCTAGCAGGATaatctcatagatcaaatataaggaggat
## [33] --
## [34] >BBa_J23116--salis-1-10
## [35] TTGACAGCTAGCTCAGTCCTAGGGACTATGCTAGCAGGATaatctcatagatcaaatataggggggat
## [36] --
## [37] >BBa_J23117--apFAB832
## [38] TTGACAGCTAGCTCAGTCCTAGGGATTGTGCTAGCCAATCatcttaatctagctggggaggcttt