For Manhattan plots and other plots where you're plotting -log10(P-values) or untransformed P-values, you sometimes want to draw line to identify when FDR=0.05 is reached. But where do you draw the line? Below is R code that identifies the nearest P-value to FDR=0.05. You can then use variable FDR5.equiv.P to create a line on your Manhattan plot.
Code assumes you have a data frame with two columns, "Pval" and "FDR".
Sometimes I have columns with duplicate values that I want to collapse into unique values. For example: comma-separated values, semicolon separated values, etc. See the "Gene Names" column below.
See also: "How to get started with R programming"
Learn to prepare an Excel spreadsheet for data import, re-save as a .csv file, load into R, look at the data, subset to significant genes, and write the smaller spreadsheet to a new .csv file.
I am updating my R version and re-installing a bunch of things. Here is the code so I can copy/paste more easily in the future.
This R code example shows how to automatically compile multiple csv spreadsheets (or csv-formatted simple Excel spreadsheets) into one multi-sheet Excel spreadsheet. Personally, I use this to combine datasets from Ingenuity Pathways Analysis for supplemental files. I can do it manually but I always worry that I'll accidentally open the wrong analysis file or mis-name the tab.
This way, I have a record of what files became what named sheets. I can also quickly re-compile a new Excel results file if I rerun the analysis by just changing the filenames in this code.
#install.packages("gdata")
#install.packages("openxlsx")
library(gdata) ## for read.xls() function; requires perl
library(openxlsx)Little things I re-use often.
timenow = function() {
time1 = format(Sys.time(),"%Y-%m-%d") #makes a date stamp
time2 = format(Sys.time(),"%H%M%p") #makes a time stamp
x = paste0(time1,"-",time2)
return(x)
} #/end function timenowtimenow()
Example output:
"2021-05-14-0825AM" |
| RStudio window showing R version 4.5.3 and working directory C:/ |
history > history.txt #saves your history to a text file, overwriting it if it already exists
history >> history.txt #saves your history to a text file, adding to the end (appending) if it already exists instead of overwriting it
ip a #prints your internet IP addresses (ethernet and wifi)
ls #shows you all the filenames in your directory
pwd #print current working directory; default is /home/username
which #shows you where a command lives (commands are programs so this helps troubleshoot if a command doesn't work)
which ls #example showing you where the ls command lives on your system
File: New: Notebook
x = 5y = 10x + y
15
z = x*x
zprint(z)
print(x+y)print("Hello world")z = "Beautiful"print("Hello",z)
print(x, type(x))print(y, type(y))print(z, type(z))
y = y+0.01print(y, type(y))
2 + 1 # addition2 - 1 # subtraction2*3 # multiplication18 / 2 # division2**3 # exponent
Adding comments is very helpful to take notes on your code. Write #comments regularly.
Relational operators:
x = 100
y = 2
x < y # less than
x > y # greater than
x <= y # less than or equal to
x >= y # greater than or equal to
x == y # double equal sign evaluates for equivalency (is x equal to y?)
x != y # is x NOT EQUAL to y?
Create ifelse statements.
x = 15
y = 10
if x > y: #Note the use of the colon to indicate the end of the if statement to be evaluated
print(str(x)+ " is greater than " +str(y)) #Code to run if statement is true
else: #What to run if the conditional statement is not true
print(str(x)+ "is " +str(y)+ "or less")
Note that Python requires correct indentation of lines for ifelse statements. Not all programming languages enforce this, but Python is strict about it.
The colons after the if conditional statement and after else are important to tell Python what to do. Python will evaluate if the conditional statement is true or not, then decide which code block to run.
Create a while loop. It repeatedly runs a loop until the conditional statement is no longer true.
iteration=0
while iteration < 5:
print("Iteration:", iteration)
iteration += 1 #increases variable 'iteration' by 1 each time the while loop is run
Be careful with while loops. If you don't create a way for it to be interrupted, you can manually stop the code with the square stop icon.
Combine conditional statements and decide if either needs to be true, or if both need to be true.
x=2
y=15
a=5
b=6
is_true = x>y or a<b
print(is_true)
is_true = x>y and a<b
print(is_true)
Copying and aliasing comparisons:
a=[2,3,4]True
False
True
Ranges:
for i in range(5):
print(i)
0
1
2
3
4
for i in range(25,30):print(i)
25
26
27
28
29
Pre-defined lists and using list indexes to pull out values:
my_list = [1, True, 3, 'Vegas', 5]
print(my_list[3])
Vegas
Because Python is zero-indexed (lists begin with zero), the list item 3 is actually the 4th item because Python counts 0,1,2,3,4.
Strings can also be lists of characters:
word = "Python"
for letter in word:
print(letter)
p
y
t
h
o
n
Use loops to add values to lists:
Long way:
squares = []
for i in range(5):
squares.append(i**2)
print(squares)
[0, 1, 4, 9, 16]
Concise way:
squares = [i**2 for i in range(5)]
print(squares)
Slice lists (get list subsets):
fruits = ["apple", "banana", "kiwi", "guava", "cherry"]
for fruit in fruits[1:-1]:
print(fruit)
banana
kiwi
guava
The code was told where to start (at index 1, which is the second value since Python starts with 0), and where to end (at index -1, which is the second-to-last spot because Python can go backwards).
Dictionaries store key-value pairs:
student = {
"name": "Jose Soandso",
"age": 20,
"major": "Math"
}
## see the dictionary
print(student)
## pull a specific value
student["age"]
## print in loop
for key, value in student.items():
print(f"{key}: {value}") #f-string formatting
Use R package "pdftools" to merge separate pdf into one pdf file. You will never need to use sketchy websites or pay for software ...
