Add the necessary code to make this script function.

Preliminaries

Load packages

library(seqinr)
library(rentrez)
library(compbio4all)
library(Biostrings)
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
## Loading required package: stats4
## 
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
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##     expand.grid, I, unname
## Loading required package: IRanges
## Loading required package: XVector
## Loading required package: GenomeInfoDb
## 
## Attaching package: 'Biostrings'
## The following object is masked from 'package:seqinr':
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##     translate
## The following object is masked from 'package:base':
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##     strsplit

Get data shroom data

Download sequence of hShroom 3 protein: NP_001166171.1

shroom3 <- rentrez::entrez_fetch(id = "NP_001166171.1",
                                      db = "protein", 
                                      rettype="fasta")

Clean and set up sequence as vector.

shroom3_vector <- fasta_cleaner(shroom3)

Confirm set up using str()

str(shroom3_vector)
##  chr [1:852] "M" "E" "A" "L" "G" "P" "G" "G" "D" "R" "A" "S" "P" "A" "S" ...

Check length - Shroom is on the big end of proteins

length(shroom3_vector)
## [1] 852

I am therefore going to subset it initially so the example plots don’t take as long to make

shroom3_vector <- shroom3_vector[1:400]

Make a 2 x 2 grid of dotplots to explore effect of changing window size and nmatch

# set up 2 x 2 grid, make margins thinner
par(mfrow = c(2,2), 
    mar = c(0,0,2,1))

# plot 1: Shroom - Defaults
dotPlot(shroom3_vector, 
        shroom3_vector, 
        wsize = 1, 
        nmatch = 1, 
        main = "Shroom Defaults")

# plot 2 Shroom - size = 10, nmatch = 1
dotPlot(shroom3_vector, shroom3_vector, 
        wsize = 10, 
        nmatch = 1, 
        main = "Shroom - size = 10, nmatch = 1")

# plot 3: Shroom - size = 10, nmatch = 5
dotPlot(shroom3_vector, shroom3_vector, 
        wsize = 10, 
        nmatch = 5, 
        main = "Shroom - size = 10, nmatch = 5")

# plot 4: size = 20, nmatch = 5
dotPlot(shroom3_vector, shroom3_vector, 
        wsize = 20,
        nmatch =5,
        main = "Shroom - size = 20, nmatch = 5")

# reset par() - run this or other plots will be small!
par(mfrow = c(1,1), 
    mar = c(4,4,4,4))