noah/CS-6643-Bioinformatics-Lab-1
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Final code edits and report

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This commit is contained in:
Noah L. Schrick 2022-09-06 23:41:26 -05:00
parent bda39896f2
commit 8e2c04a699
4 changed files with 7 additions and 5 deletions
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.~lock.Schrick-Noah_CS-6643_Lab1-Report.doc#
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Schrick-Noah_CS-6643_Lab1.R
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@ -32,7 +32,7 @@ pie(my.dna.table.df$Freq, labels = my.dna.table.df$label, col = cols,
main = "Pie Chart Representation of Random ACTG Sample")
bp <- barplot(as.matrix(my.dna.table), beside = TRUE, xlab = "Letter",
bp <- barplot(as.matrix(my.dna.table), beside = TRUE, xlab = "Nucleotide",
ylab = "Frequency", ylim = c(-1, max(as.numeric(my.dna.table))+2),
main = "Bar Plot Representation of Random ACTG Sample", col = cols,
legend = TRUE)
@ -69,7 +69,6 @@ fasta2vec <- function(fasta.file){
fasta.string <- fasta[[1]][1]
fasta.list <- strsplit(fasta.string,"")
fasta.vec <- unlist(fasta.list)
}
fasta.vec <- fasta2vec("apoe.fasta")
@ -93,7 +92,8 @@ fasta.bp <- barplot(as.matrix(fasta.table), beside = TRUE, xlab = "Letter",
col = fasta.cols, legend = TRUE)
text(x = fasta.bp, y = 1.1*fasta.table, labels = as.numeric(fasta.table))
text(x = fasta.bp, y = -0.10*max(as.numeric(fasta.table)), labels = names(fasta.table))
text(x = fasta.bp, y = -0.10*max(as.numeric(fasta.table)),
labels = names(fasta.table))
## g
fasta.nuc_prob <- fasta.table/fasta.len
@ -138,10 +138,13 @@ compare.bp <- barplot(as.matrix(compare.bind), beside = TRUE,
ylim = c(-0.0,
1.25*max(c(fasta.nuc_prob, covid.nuc_prob))),
main = "Bar Plot Representation and Comparison of APOE to COVID Nucleotide Probabilities",
legend = TRUE)
legend = TRUE, legend.text = c("APOE", "COVID"))
ycords = 1.03*c(rbind(as.vector(fasta.nuc_prob), as.vector(covid.nuc_prob)))
tlabs = c(rbind(as.vector(fasta.nuc_prob), as.vector(covid.nuc_prob)))
text(x = compare.bp, y = ycords,
labels = round(as.numeric(tlabs), digits = 3))
## b
covid.gc <- GC(covid.vec)