ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

data in ./myScripts/

Browse Source
This commit is contained in:
hyginn 2020-10-02 18:50:36 +10:00
parent 3173aec119
commit 152d01273f
1 changed files with 31 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

46
BIN-FUNC-Domain_annotation.R
View File

@ -3,18 +3,20 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-FUNC-Domain_annotation unit. # R code accompanying the BIN-FUNC-Domain_annotation unit.
# #
# Version: 1.1 # Version: 1.2
# #
# Date: 2017-11 - 2020-09 # Date: 2017-11 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.2 Consistently: data in ./myScripts/ ;
# begin SHARING DATA section
# 1.1 2020 Updates # 1.1 2020 Updates
# 1.0 Live version 2017 # 1.0 Live version 2017
# 0.1 First code copied from 2016 material. # 0.1 First code copied from 2016 material.
# #
# TODO: # TODO:
# # Complete SHARING DATA section ...
# #
# == DO NOT SIMPLY source() THIS FILE! ======================================= # == DO NOT SIMPLY source() THIS FILE! =======================================
# #
@ -26,7 +28,7 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------------------------- #TOC> ---------------------------------------------------------------------
#TOC> 1 Update your database script 42 #TOC> 1 Update your database script 42
@ -35,7 +37,7 @@
#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 97 #TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 97
#TOC> 1.2 Execute and Validate 124 #TOC> 1.2 Execute and Validate 124
#TOC> 2 Plot Annotations 149 #TOC> 2 Plot Annotations 149
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -54,10 +56,10 @@
# IF YOU HAVE NOT YET COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT: # IF YOU HAVE NOT YET COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
# #
# You DON'T already have a file called "<MYSPE>-Annotations.json" in the # You DON'T already have a file called "<MYSPE>-Annotations.json" in the
# ./data/ directory: # ./myScripts/ directory:
# #
# - Make a copy of the file "./data/refAnnotations.json" and put it in your # - Make a copy of the file "./data/refAnnotations.json" and put it in your
# project directory. # myScripts/ directory.
# #
# - Give it a name that is structured like "<MYSPE>-Annotations.json" - e.g. # - Give it a name that is structured like "<MYSPE>-Annotations.json" - e.g.
# if MYSPE is called "Crptycoccus neoformans", your file should be called # if MYSPE is called "Crptycoccus neoformans", your file should be called
@ -79,27 +81,30 @@
# and change the "start" and "end" features to the coordinates you # and change the "start" and "end" features to the coordinates you
# recorded in the SMART database. # recorded in the SMART database.
# #
# - Save your file. # - Save your file in the ./myScripts/ folder.
# #
# - Validate your file online at https://jsonlint.com/ # - Validate your file online at https://jsonlint.com/
# #
# - Update your "makeProteinDB.R" script to load your new # - Update your "./myScripts/makeProteinDB.R" script to load your new
# annotation when you recreate the database. Open the script in the # annotation when you recreate the database. Open the script in the
# RStudio editor, and add the following command at the end: # RStudio editor, and add the following command at the end:
# #
# myDB <- dbAddAnnotation(myDB, fromJSON("<MYSPE>-Annotations.json")) # myDB <- dbAddAnnotation(myDB,
# jsonlite::fromJSON("./myScripts/<MYSPE>-Annotations.json"))
# ^^^^^^^
# edit this!
# #
# - save and close the file. # - save and close the file.
# #
# Then SKIP the next section. # Then SKIP the next section.
# #
# #
# === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" # === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment"
# #
# IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT: # IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
# #
# You SHOULD have a file called "<MYSPE>-Annotations.json" in the # You SHOULD have a file called "<MYSPE>-Annotations.json" in the
# ./data/ directory: # ./myScripts/ directory:
# #
# - Open the file in the RStudio editor. # - Open the file in the RStudio editor.
# #
@ -109,7 +114,7 @@
# - Add a comma after every line except for the last one # - Add a comma after every line except for the last one
# #
# - Edit the annotations but include only features that are in the # - Edit the annotations but include only features that are in the
# myDB$feature table. Check which features are in the databse by executing # myDB$feature table. Check which features are in the database by executing
# #
# myDB$feature$name # myDB$feature$name
# #
@ -125,7 +130,7 @@
# #
# - source() your database creation script: # - source() your database creation script:
# #
# source("makeProteinDB.R") # source("./myScripts/makeProteinDB.R")
# #
# This should run without errors or warnings. If it doesn't work and you # This should run without errors or warnings. If it doesn't work and you
# can't figure out quickly what's happening, ask for help on the # can't figure out quickly what's happening, ask for help on the
@ -228,7 +233,7 @@ xMax <- max(nchar(myDB$protein$sequence[iRows])) * 1.1 # longest sequence
# plot an empty frame # plot an empty frame
oPar <- par(mar = c(4.2, 0.1, 3, 0.1)) # save the current plot parameters and oPar <- par(mar = c(4.2, 0.1, 3, 0.1)) # save the current plot parameters and
# decrease margins # decrease margins
plot(1, 1, plot(1, 1,
xlim = c(-200, xMax + 100), xlim = c(-200, xMax + 100),
ylim = c(0, yMax), ylim = c(0, yMax),
@ -271,5 +276,16 @@ par(oPar) # reset the plot parameters
# It would be better to align the motif borders, at least approximately (not # It would be better to align the motif borders, at least approximately (not
# all proteins have all motifs). How would you go about doing that? # all proteins have all motifs). How would you go about doing that?
# = 1 SHARING DATA ======
# It's particularly interesting to compare such annotations across many
# homologous proteins. I have created a file on the student Wiki that you can
# edit, and then download the data from the entire class directly to your
# RStudio project.
#
# Task:
# =====
# Navigate to
# [END] # [END]