russelllab / kinaseresistance Goto Github PK
View Code? Open in Web Editor NEWA method to predict activating, deactivating and resistance mutations in kinases
Home Page: http://activark.russelllab.org
License: GNU General Public License v3.0
A method to predict activating, deactivating and resistance mutations in kinases
Home Page: http://activark.russelllab.org
License: GNU General Public License v3.0
Draw a GRID violin plot to describe the role of each feature i.e. show multiple features in the same plot.
Write tests for both webApp and command-line
Use embeddings from Uniprot as features
MAP2K3
P46734/S218E
P46734/T222E
Actually, multiple newlines cause a crash I think."
refer point 2
https://agrussell.slack.com/archives/C04P305PK61/p1682938480543719
Let's go with colour-blind-friendly shades.
The top one (red/orange) is deactivating
Third from the top (bluish) is resistance
the bottom-most one (greenish) is activating
I can fx this in my scripts and can you do this in yours?
@gurdeep330 told me that Rob
"wants the ADR heatmap to NOT change i.e. it should be done for the entire alignment (>400 kinases) even if the user is looking at top 10 or 20, say"
The most efficient solution I could think of immediately would be to do the counts for the 'heatmap' separately and read it from a dictionary (using alignment positions rather than protein positions I think) rather than going through each letter of the whole alignment to sum up the values, each time we recalculate/redraw the alignment.
Collect all possible features and create an FM (feature matrix) to be used for ML
https://agrussell.slack.com/archives/C04P305PK61/p1683191322269059
Point 6, can you introduce another parameter in the main function that tells how to sort the genes in the alignment?
z.B.
At the front end, I will create a drop-down menu, from which the user selects the type of sort, and then I call the same main
function.
I think you can use the PostgreSQL DB to fetch the fasta sequences and PTM information. You can connect to the DB in your code:
import psycopg2
def connection():
'''Function to connect to postgresql database'''
mydb = psycopg2.connect(
database = "kinase_project",
user = "gurdeep",
password = "hellokitty",
host = "localhost",
port = "5432")
return mydb
mydb = connection()
mydb.autocommit = True
mycursor = mydb.cursor()
and from the command-line on pevolution2: psql -U gurdeep kinase_project
Let me know if I can provide or do something else or if you have a better alternative in mind. :-)
Create an alignment based on what is around the given position of interest or by selecting kinases that have the most information.
Say in the info box if the position is upstream or downstream or the same position. Use some labels in HTML? Same for variants too.
hmmalign
of all the candidates and prepare an output aln#41 is also fixed. Follow the comments below to update the alignment
Other little things for the WebApp (some of these are repetitions, but people under 40 apparently do not ever read anything that isn't in a tweet - according to some podcast I just heard - so...)
we want sections about prior info below the name:
https://stackoverflow.com/questions/37121767/svg-with-clickable-links-in-shiny-not-clickable
re:svg, I was looking this up for my shiny application today and people seem to recommend incorporating svgs via "".
It did not work for RShiny (I found another way to do it there) but otherwise seemed to be a promising approach.
Error handling for both webApp and command-line z.B. if gene or ACC does not exist, if the position is outside domain
Write a short tutorial like in precog(x)
@tschmenger
So Rob suggested having the mouseover information in the Mechismo format z.B.
kinase/WTpos; mt_type
EGFR/T790; R
T is the WT AA and R is the mutation type
Add active links for p-sits and known variants. Remove "ECO" etc from the info and just have the text and the link.
z.B. BRAF/V600E is missing
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