145 lines
5.4 KiB
R
145 lines
5.4 KiB
R
# tocID <- "BIN-MYSPE.R"
|
|
#
|
|
# ---------------------------------------------------------------------------- #
|
|
# PATIENCE ... #
|
|
# Do not yet work wih this code. Updates in progress. Thank you. #
|
|
# boris.steipe@utoronto.ca #
|
|
# ---------------------------------------------------------------------------- #
|
|
#
|
|
# Purpose: A Bioinformatics Course:
|
|
# R code accompanying the BIN-MYSPE unit
|
|
#
|
|
# Version: 1.1
|
|
#
|
|
# Date: 2020-09-18
|
|
# Author: Boris Steipe (boris.steipe@utoronto.ca)
|
|
#
|
|
# V 1.1 2020 Workflow changes
|
|
# V 1.0.1 Move ABC-makeMYSPElist.R to ./scripts directory
|
|
# V 1.0 Final code, after rewriting BLAST parser and updating MYSPElist
|
|
# V 0.1 First code copied from BCH441_A03_makeMYSPElist.R
|
|
#
|
|
# TODO:
|
|
#
|
|
#
|
|
# == HOW TO WORK WITH LEARNING UNIT FILES ======================================
|
|
#
|
|
# DO NOT SIMPLY source() THESE FILES!
|
|
#
|
|
# If there are portions you don't understand, use R's help system, Google for an
|
|
# answer, or ask your instructor. Don't continue if you don't understand what's
|
|
# going on. That's not how it works ...
|
|
#
|
|
# ==============================================================================
|
|
|
|
|
|
#TOC> ==========================================================================
|
|
#TOC>
|
|
#TOC> Section Title Line
|
|
#TOC> -----------------------------------------------
|
|
#TOC> 1 Preparations 47
|
|
#TOC> 2 Suitable MYSPE Species 59
|
|
#TOC> 3 Adopt "MYSPE" 83
|
|
#TOC>
|
|
#TOC> ==========================================================================
|
|
|
|
|
|
# = 1 Preparations ========================================================
|
|
#
|
|
|
|
# Execute the two conditionals below:
|
|
if (! file.exists("scripts/.myProfile.R")) {
|
|
stop("PANIC: profile file does not exist. Fix problem or ask for help.")
|
|
}
|
|
if (! exists("myStudentNumber")) {
|
|
stop("PANIC: profile data wasn't loaded. Fix problem or ask for help.")
|
|
}
|
|
|
|
|
|
# = 2 Suitable MYSPE Species ==============================================
|
|
|
|
|
|
# In this unit we will select one species from a list of genome sequenced fungi
|
|
# and write it into your personalized profile file. This species will be called
|
|
# "MYSPE" (Your Favourite Organism) for other learning units and exercises.
|
|
|
|
# A detailed description of the process of compiling the list of genome
|
|
# sequenced fungi with protein annotations and Mbp1 homologues is in the file
|
|
# ./scripts/ABC-makeMYSPElist.R In brief, data for genome-sequenced fungi
|
|
# was retrieved from https://fungi.ensembl.org; a search for homologues to
|
|
# yeast Mbp1 was performed with BLAST at the NCBI, and the data was merged.
|
|
# A representative organism at each genus-level was chosen from those hits
|
|
# that actual;ly have a homologue. Finally, a mapping table was constructed to
|
|
# asymmetrically retrieve unique species: a student number will retrieve
|
|
# a species, but (public) knowledge of the species cannot reconstruct the
|
|
# student number.
|
|
|
|
# Task: Study ./scripts/ABC-makeMYSPElist.R, it implements a typical workflow
|
|
# of selecting and combining data from various data resources. Studying
|
|
# it will give you a better sense of how such workflows can be
|
|
# implemented in practice.
|
|
|
|
|
|
# = 3 Adopt "MYSPE" =======================================================
|
|
|
|
# Execute:
|
|
( MYSPE <- getMYSPE(myStudentNumber) )
|
|
|
|
# If this produced an error, this session has not been properly set up. You
|
|
# may not yet have run init() and edited .myProfile.R , or that file is not
|
|
# in your myScripts/ folder. Fix this, and execute source(".Rprofile") .
|
|
|
|
# If this produced NA, your Student Number may not be correct, or you are not
|
|
# in my class-list. Contact me.
|
|
# Otherwise, this should have printed a species name. Your unique species
|
|
# for this course.
|
|
|
|
biCode(MYSPE) # and what is it's "BiCode" ... ?
|
|
|
|
# Task: Note down the species name and its five letter BiCode on your Student
|
|
# Wiki user page. Use this species whenever this or future assignments refer
|
|
# to MYSPE. Whenever you start a session, it will automatically be loaded
|
|
# from myScripts/.myProfile.R and is available as MYSPE .
|
|
|
|
# Here is some more information:
|
|
fungiDat <- read.csv("data/Species.csv")
|
|
|
|
# number of sequenced fungal genomes:
|
|
nrow(fungiDat)
|
|
|
|
# sequenced genomes of species:
|
|
sel <- MYSPE == gsub("^(\\S+\\s\\S+).*$", "\\1", fungiDat$Name)
|
|
( x <- fungiDat[sel, "Name"] )
|
|
Nspc <- length(x) # save this for later ...
|
|
|
|
# sequenced genomes of genus:
|
|
sel <- gsub("\\s.*", "", MYSPE) == gsub("\\s.*", "", fungiDat$Name)
|
|
( x <- fungiDat[sel, "Name"] )
|
|
Ngen <- length(x) - Nspc
|
|
|
|
# order:
|
|
( x <- unique(fungiDat[sel, "Classification"]) )
|
|
Nord <- sum(fungiDat$Classification == x) - Ngen - Nspc
|
|
Nfng <- nrow(fungiDat) - Nord - Ngen - Nspc
|
|
|
|
# proportions
|
|
pCol <- c("#ed394e", "#ff9582", "#ffd5c4", "#f2f2f0")
|
|
pie(c(Nspc, Ngen, Nord, Nfng),
|
|
labels = "",
|
|
radius = 1,
|
|
main = "MYSPE in genome-sequenced fungi",
|
|
sub = MYSPE,
|
|
col = pCol,
|
|
clockwise = TRUE,
|
|
init.angle = 90)
|
|
legend(x = 1.3, y = 0.8, # position
|
|
legend = c("Species", "Genus", "Order", "Fungi"),
|
|
y.intersp = 1.5, # line spacing for labels
|
|
cex = 0.9, # character size for labels
|
|
bty = "n", # "no" box around the legend
|
|
pt.cex = 2, # size of colour boxes
|
|
pch = 15,
|
|
col = pCol)
|
|
|
|
# [END]
|