I'm trying to create a for loop in R to iterate through a list of genetic variants, labeled with rsID's, and filter the results by patient ID.
ace2_snps <- c("rs4646121", "rs4646127", "rs1996225", "rs2158082", "rs4830974", "rs148271868", "rs113539251", "rs4646135", "rs4646179", "rs2301693", "rs16980031", "rs12689012", "rs4646141", "rs142049267", "rs16979971", "rs12007623", "rs4646182", "rs147214574", "rs6632677", "rs139469582", "rs149000434", "rs148805807", "rs112032651", "rs144314464", "rs147077778", "rs182259051", "rs112621533", "rs35803318", "rs35304868", "rs113848176", "rs145345877", "rs12009805", "rs233570", "rs73635824", "rs73635823", "rs4646142", "rs4646157", "rs2074192", "rs79878075", "rs144239059", "rs67635467", "rs183583165", "rs137910448", "rs116419580", "rs2097723", "rs4646170")
for (snps in ace2_snps) {
genotype_snps <- as.data.frame(bgen_ACE2$data[snps,,])
idfromcsv <- read.csv("/Users/keeseyyyyy/Desktop/Walley/pospatid.csv")
id <- as.character(idfromcsv[[1]])
filtered_snps <- genotype_snps[id,] }
I need to run genotype_rs146217251 <- as.data.frame(bgen_ACE2$data["rs146217251",,]) for each rsID, and then I'd like to label the variable filtered_snps according to its rsID in the place of "snps" in the variable name for each variant.
I'm not very familiar with R syntax. Can anyone give me some tips?
For one variant, the process would go like this:
genotype_rs146217251 <- as.data.frame(bgen_ACE2$data["rs146217251",,])
idfromcsv <- read.csv("/Users/keeseyyyyy/Desktop/Walley/pospatid.csv")
id <- as.character(idfromcsv[[1]])
filtered <- genotype_rs146217251[id,]
Related
I am trying to find Cronbach's Alpha for survey data containing a series of multi-item measures. Rather than have to manually write out every single multi-item measure, it looks like something a loop should be able to manage far more effectively, but it needs to change only part of the column name, according to the question number.
The basic idea as it currently sits in my head would be...
for (N in 4:22) {
ytqN <- data.frame(YT_Data$QNa, YT_Data$QNb, YT_Data$QNc)
alpha(ytqN)
}
The loop would then create new data frames for each multi item measure and run Cronbach's Alpha as it goes.
This doesn't work though. :(
ytq4 <- data.frame(YT_Data$Q4a, YT_Data$Q4b, YT_Data$Q4c)
alpha(ytq4)
ytq5 <- data.frame(YT_Data$Q5a, YT_Data$Q5b, YT_Data$Q5c)
alpha(ytq5)
ytq6 <- data.frame(YT_Data$Q6a, YT_Data$Q6b, YT_Data$Q6c)
alpha(ytq6)
ytq7 <- data.frame(YT_Data$Q7a, YT_Data$Q7b, YT_Data$Q7c)
alpha(ytq7)
ytq8 <- data.frame(YT_Data$Q8a, YT_Data$Q8b, YT_Data$Q8c)
alpha(ytq8)
ytq9 <- data.frame(YT_Data$Q9a, YT_Data$Q9b, YT_Data$Q9c)
alpha(ytq9)
ytq10 <- data.frame(YT_Data$Q10a, YT_Data$Q10b, YT_Data$Q10c)
alpha(ytq10)
ytq11 <- data.frame(YT_Data$Q11a, YT_Data$Q11b, YT_Data$Q11c)
alpha(ytq11)
ytq12 <- data.frame(YT_Data$Q12a, YT_Data$Q12b, YT_Data$Q12c)
alpha(ytq12)
ytq13 <- data.frame(YT_Data$Q13a, YT_Data$Q13b, YT_Data$Q13c)
alpha(ytq13)
ytq14 <- data.frame(YT_Data$Q14a, YT_Data$Q14b, YT_Data$Q14c)
alpha(ytq14)
ytq15 <- data.frame(YT_Data$Q15a, YT_Data$Q15b, YT_Data$Q15c)
alpha(ytq15)
ytq16 <- data.frame(YT_Data$Q16a, YT_Data$Q16b, YT_Data$Q16c)
alpha(ytq16)
ytq17 <- data.frame(YT_Data$Q17a, YT_Data$Q17b, YT_Data$Q17c)
alpha(ytq17)
ytq18 <- data.frame(YT_Data$Q18a, YT_Data$Q18b, YT_Data$Q18c)
alpha(ytq18)
ytq19 <- data.frame(8 - YT_Data$Q19a, YT_Data$Q19b, YT_Data$Q19c)
# Reverse code Q19a
alpha(ytq19)
ytq20 <- data.frame(YT_Data$Q20a, YT_Data$Q20b, YT_Data$Q20c)
alpha(ytq20)
ytq21 <- data.frame(YT_Data$Q21a, YT_Data$Q21b, YT_Data$Q21c)
alpha(ytq21)
ytq22 <- data.frame(YT_Data$Q22a, YT_Data$Q22b, YT_Data$Q22c)
alpha(ytq22)
The desired results would be a single output containing all the Cronbach's Alphas for the multi item measures for questions 4-22 in the data set I am currently working on executed via a single piece of code, rather than have to go question by question.
It's easier to help if you include your data, but I guess this should work:
alpha_list = list()
for(N in 4:22){
ytq = data.frame(YT_Data[paste0("Q",N,"a")],
YT_Data[paste0("Q",N,"b")],
YT_Data[paste0("Q",N,"c")])
alpha_list[[N]] = alpha(ytq)
}
We are using paste0() to create the column names while looping on N. alpha_list will be a list with the results given by alpha()
I have created a grid.table object to display a dataframe in PowerBi, below there is my code:
dataset <- data.frame(BDS_ID = c("001","002"),
PRIORITY = c("high","medium"),
STATUS = c("onair","onair"),
COMPANY = c("airfr","fly"))
my.result <- melt(dataset, id = c("BDS_ID"))
mytheme <- ttheme_default(base_size = 10,
core=list(fg_params=list(hjust=0, x=0.01),
bg_params=list(fill=c("white", "grey90"))))
for (i in 1:nrow(tg)) {
tg$grobs[[i]] <- editGrob(tg$grobs[[i]], gp=gpar(fontface="bold"))
}
grid.draw(tg)
and this is my output:
I would like to improve my output in the following way: I would like that the row headers to be unique and have a different column for each different value of each variable repeating the column with the row headers each time.
I tried to do this using the statement t(dataset), but I do not get the desired result because the row headers are not repeated.
I would like to get an output (always classy grob) similar to this:
**PRIORITY** high **PRIORITY** medium
**STATUS** onair **STATUS** onair
**COMPANY** airfr **COMPANY** fly
Does anyone knows how to achive this?
Thanks
I'm unable to reproduce the grob format you've shown based on the code you've provided, but I've got something similar:
dataset <- data.frame(BDS_ID = c("001","002"),
PRIORITY = c("high","medium"),
STATUS = c("onair","onair"),
COMPANY = c("airfr","fly"))
dataset <- data.frame(t(dataset))
dataset$label1 <- rownames(dataset)
dataset$label2 <- rownames(dataset)
colnames(dataset) <- c("status1", "status2", "label1", "label2")
dataset <- dataset[c(2:nrow(dataset)), c(3, 1, 4, 2)]
rownames(dataset) <- NULL
test <- grid.draw(tableGrob(dataset))
The above code produces the following object. It doesn't look exactly like yours, but it's in the general structure you're looking for:
I'm using the R package rnoaa(along with it required other packages) to gather historical weather data. I wrote this nestled loop to gather all the data sets but I keep getting errors when I run it. It seems to run for a second fine
The loop:
require('triebeard')
require('bindr')
require('colorspace')
require('mime')
require('curl')
require('openssl')
require('R6')
require('urltools')
require('httpcode')
require('stringr')
require('assertthat')
require('bindrcpp')
require('glue')
require('magrittr')
require('pkgconfig')
require('rlang')
require('Rcpp')
require('BH')
require('plogr')
require('purrr')
require('stringi')
require('tidyselect')
require('digest')
require('gtable')
require('plyr')
require('reshape2')
require('lazyeval')
require('RColorBrewer')
require('dichromat')
require('munsell')
require('labeling')
require('viridisLite')
require('data.table')
require('rjson')
require('httr')
require('crul')
require('lubridate')
require('dplyr')
require('tidyr')
require('ggplot2')
require('scales')
require('XML')
require('xml2')
require('jsonlite')
require('rappdirs')
require('gridExtra')
require('tibble')
require('isdparser')
require('geonames')
require('hoardr')
require('rnoaa')
install.package('ncdf4')
install.packages("devtools")
library(devtools)
install_github("rnoaa", "ropensci")
library(rnoaa)
list <- buoys(dataset='wlevel')
lid <- data.frame(list$id)
foo <- for(range in 1990:2017){
for(bid in lid){
bid_range <- buoy(dataset = 'wlevel', buoyid = bid, year = range)
bid.year.data <- data.frame(bid.year$data)
write.csv(bid.year.data, file='cwind/bid_range.csv')
}
}
The response:
Using c1990.nc
Using
Error: length(url) == 1 is not TRUE
It saves the first data-set but it does not apply the for in the file name it just names it bid_range.csv.
This error message shows that there are no any data of a given station id in 1990. Because you were using for loop, once it gots an error, it stops.
Here I introduce the use of tidyverse to download the NOAA buoy data. A lot of the following functions are from the purrr package, which is part of the tidyverse.
# Load packages
library(tidyverse)
library(rnoaa)
Step 1: Create a "Grid" containing all combination of id and year
The expand function from tidyr can create the combination of different values.
data_list <- buoys(dataset = 'wlevel')
data_list2 <- data_list %>%
select(id) %>%
expand(id, year = 1990:2017)
Step 2: Create a "safe" version that does not break when there is no data.
Also make this function suitable for the map2 function
Because we will use map2 to loop through all the combination of id and year using the map2 function by its .x and .y argument. We modified the sequence of argument to create buoy_modify. We also use the safely function to create a safe version of buoy_modify. Now when it meets error, it will store the error message and moves to the next one rather than breaks.
# Modify the buoy function
buoy_modify <- function(buoyid, year, dataset, ...){
buoy(dataset, buoyid = buoyid, year = year, ...)
}
# Creare a safe version of buoy_modify
buoy_safe <- safely(buoy_modify)
Step 3: Apply the buoy_safe function
wlevel_data <- map2(data_list2$id, data_list2$year, buoy_safe, dataset = "wlevel")
# Assign name for the element in the list based on id and year
names(wlevel_data) <- paste(data_list2$id, data_list2$year, sep = "_")
After this step, all the data were downloaded in wlevel_data. Each element in wlevel_data has two parts. $result shows the data if the download is successful, otherwise, it shows NULL. $error shows NULL if the download is successful, otherwise, it shows the error message.
Step 4: Access the data
transpose can turn a list "inside out". So now wlevel_data2 has two elements: result and error. We can store these two and access the data.
# Turn the list "inside out"
wlevel_data2 <- transpose(wlevel_data)
# Get the error message
wlevel_error <- wlevel_data2$error
# Get he result
wlevel_result <- wlevel_data2$result
# Remove NULL element in wlevel_result
wlevel_result2 <- wlevel_result[!map_lgl(wlevel_result, is.null)]
Improve the following code by rewriting to be more compact (a one-liner with alply or similar?) Also if it can be made more performant (if possible).
I have a dataframe with several categorical variables, each with various number of levels. (Examples: T1_V4: B,C,E,G,H,N,S,W and T1_V7: A,B,C,D )
For any specific one of those categorical vars, I want to do the following:
Construct all possible level-permutations e.g. using DescTools::Permn()
Then for each level.perm in those level.perms...
Construct a list of function results where we apply some function to level.perm (in my particular case, recode the factor levels using level.perms, then take as.numeric, then compute correlation wrt some numeric response variable)
Finally, name that list with the corresponding string-concatenated values of level.perm (e.g. 'DBCA')
Example at bottom for permutations of A,B,C,D
Reproducible example at bottom:
The following code does this, can you improve on it? (I tried alply)
require(DescTools)
level.perms <- Permn(levels(MyFactorVariable))
tmp <- with(df,
apply( level.perms, 1,
function(var.levels) {
cor(MyResponseVariable,
as.numeric(factor(MyFactorVariable, levels=var.levels)))
})
)
names(tmp) <- apply(level.perms, 1, paste, collapse='')
Example (for CategVar1 with levels A,B,C,D):
ABCD BACD BCAD ACBD CABD CBAD BCDA ACDB
0.031423 0.031237 0.002338 0.002116 -0.026496 -0.026386 -0.008743 -0.009104
CADB CBDA ABDC BADC CDAB CDBA ADBC BDAC
-0.037228 -0.037364 0.048423 0.048075 -0.048075 -0.048423 0.037364 0.037228
BDCA ADCB DABC DBAC DBCA DACB DCAB DCBA
0.009104 0.008743 0.026386 0.026496 -0.002116 -0.002338 -0.031237 -0.031423
Reproducible example using randomly-generated dataframe:
set.seed(120)
df = data.frame(ResponseVar = exp(runif(1000, 0,4)),
CategVar1 = factor(sample(c('A','B','C','D'), 1000, replace=T)),
CategVar2 = factor(sample(c('B','C','E','G','H','N'), 1000, replace=T)) )
cor(as.numeric(df$CategVar1), df$MyResponseVar)
# 0.03142
cor(as.numeric(df$CategVar2), df$MyResponseVar)
# 0.02112
#then if you run the above code you get the above table of correlation values
I am developing a GUI using R and GTK2 and created something as shown in the photo.
Here's the script:
library(RGtk2)
rm(list=ls())
window.master <- gtkWindow("toplevel",show=FALSE)
window.master$setDefaultSize(1024,768)
window.master$set(title="Window Name")
forms.notebook <- gtkNotebook()
forms.notebook$setTabPos("top")
form1.notebook <- gtkNotebook()
form1.notebook$setTabPos("top")
form1.boxp1.y3 <- gtkVBox(FALSE,3)
form1.framep1y1 <- gtkFrame("AAA")
form1.boxp1y1.2y <- gtkVBox(FALSE,2)
form1.boxp1y1.y1.4x <- gtkHBox(FALSE,4)
form1.boxp1y1.y1.4x$packStart(gtkLabel("BBB"),FALSE,FALSE)
form1.boxp1y1.y1.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y1.4x$packStart(gtkLabel("CCC"),FALSE,FALSE)
form1.boxp1y1.y1.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y2.4x <- gtkHBox(FALSE,4)
form1.boxp1y1.y2.4x$packStart(gtkLabel("DDD"),FALSE,FALSE)
form1.boxp1y1.y2.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y2.4x$packStart(gtkLabel("EEE"),FALSE,FALSE)
form1.boxp1y1.y2.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.2y$add(form1.boxp1y1.y1.4x)
form1.boxp1y1.2y$add(form1.boxp1y1.y2.4x)
form1.framep1y1$add(form1.boxp1y1.2y)
form1.framep1y2 <- gtkFrame("FFF")
form1.boxp1y2.2y <- gtkVBox(FALSE,2)
### 1nd row ###
form1.boxp1y1.y1.6x <- gtkHBox(FALSE,6)
form1.boxp1y1.y1.6x$packStart(gtkLabel("GGG"),FALSE,FALSE)
form1.boxp1y1.y1.6x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y1.6x$packStart(gtkLabel("HHH"),FALSE,FALSE)
form1.boxp1y1.y1.6x$packStart(gtkEntry(),FALSE,FALSE)
form1.boxp1y1.y1.6x$packStart(gtkLabel("III"),FALSE,FALSE)
form1.boxp1y1.y1.6x$packStart(gtkEntry(),FALSE,FALSE)
### 2nd row ###
form1.boxp1y1.y2.4x <- gtkHBox(FALSE,4)
form1.boxp1y1.y2.4x$packStart(gtkLabel("JJJ"),FALSE,FALSE)
form1.boxp1y1.y2.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y2.4x$packStart(gtkLabel("KKK"),FALSE,FALSE)
form1.boxp1y1.y2.4x$packStart(gtkEntry(),TRUE,TRUE)
### 3nd row ###
form1.boxp1y1.y3.4x <- gtkHBox(FALSE,4)
form1.boxp1y1.y3.4x$packStart(gtkLabel("LLL"),FALSE,FALSE)
form1.boxp1y1.y3.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y1.y3.4x$packStart(gtkLabel("MMM"),FALSE,FALSE)
form1.boxp1y1.y3.4x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y2.2y$add(form1.boxp1y1.y1.6x)
form1.boxp1y2.2y$add(form1.boxp1y1.y2.4x)
form1.boxp1y2.2y$add(form1.boxp1y1.y3.4x)
form1.framep1y2$add(form1.boxp1y2.2y)
form1.framep1y3 <- gtkFrame("NNN")
form1.boxp1y3.2y <- gtkVBox(FALSE,2)
### 1nd row ###
form1.boxp1y3.y1.6x <- gtkHBox(FALSE,6)
form1.boxp1y3.y1.6x$packStart(gtkLabel("OOO"),FALSE,FALSE)
form1.boxp1y3.y1.6x$packStart(gtkEntry(),TRUE,TRUE)
form1.boxp1y3.y1.6x$packStart(gtkLabel("PPP"),FALSE,FALSE)
form1.boxp1y3.y1.6x$packStart(gtkEntry(),FALSE,FALSE)
form1.boxp1y3.y1.6x$packStart(gtkLabel("QQQ"),FALSE,FALSE)
form1.boxp1y3.y1.6x$packStart(gtkEntry(),FALSE,FALSE)
### 2nd row ###
form1.boxp1y3.y2.2x <- gtkHBox(FALSE,2)
form1.boxp1y3.y2.2x$packStart(gtkCheckButton("RRR"),TRUE,TRUE)
form1.boxp1y3.y2.2x$packStart(gtkCheckButton("SSS"),TRUE,TRUE)
form1.boxp1y3.2y$add(form1.boxp1y3.y1.6x)
form1.boxp1y3.2y$add(form1.boxp1y3.y2.2x)
form1.framep1y3$add(form1.boxp1y3.2y)
form1.boxp1.y3$packStart(form1.framep1y1,FALSE,FALSE)
form1.boxp1.y3$packStart(form1.framep1y2,FALSE,FALSE)
form1.boxp1.y3$packStart(form1.framep1y3,FALSE,FALSE)
form1.boxp2.ud <- gtkVBox(FALSE,2)
form1.framep2f1 <- gtkFrame("TTT")
form1.framep2f2 <- gtkFrame("UUU")
form1.boxp2.ud$add(form1.framep2f1)
form1.boxp2.ud$add(form1.framep2f2)
form1.boxp3.ud <- gtkVBox(FALSE,1)
form1.framep3f1 <- gtkFrame("VVV")
form1.boxp3.ud$add(form1.framep3f1)
form1.boxp4.ud <- gtkVBox(FALSE,1)
form1.framep4f1 <- gtkFrame("WWW")
form1.boxp4.ud$add(form1.framep4f1)
form1.boxp5.ud <- gtkVBox(FALSE,1)
form1.framep5f1 <- gtkFrame("XXX")
form1.boxp5.ud$add(form1.framep5f1)
form1.notebook$add(form1.boxp1.y3)
form1.notebook$add(form1.boxp2.ud)
form1.notebook$add(form1.boxp3.ud)
form1.notebook$add(form1.boxp4.ud)
form1.notebook$add(form1.boxp5.ud)
forms.notebook$add(form1.notebook)
window.master$add(forms.notebook)
window.master$show()
I have a few questions:
How to change the tab name? (I can't use Page1,Page2,Page3 everywhere)
How to add spacer between each row/frame?
I want to display information from the dataframe into the gtkEntry field, I think I need to give label of the gtkEntry field, how can I do that?
Thanks.
A few answers:
How to change the tab name? (I can't use Page1,Page2,Page3 everywhere):
Instead of form1.notebook$add(form1.boxp1.y3) use form1$appendPage() with the tab.label option. See ?gtkNotebookAppendPage
How to add spacer between each row/frame?
For a layout like this you should be using gtkTable. For gtkVBox you can use setSpacing (?gtkBoxSetSpacing and/or padding when packing.
I want to display information from the dataframe into the gtkEntry field, I think I need to give label of the gtkEntry field, how can I do that?
Not sure what you want to do here. I'm guessing you want to a) name your gtkEntry objects and then set their text. If you coordinate your names with your data frame this can be done quickly. For example, using a list to store the entries along the lines of (from your BBB label):
l <- list()
form1.boxp1y1.y1.4x$packStart(l$BBB <- gtkEntry(),TRUE,TRUE) ## BBB from your label
etc.
Then supposing your data frame has a column BBB (along with others) you can do something like
sapply(names(l), function(i) l[[i]]$setText(your_dataframe[1,i]))
Or if you don't like so many ['s you could use:
mapply(gtkEntrySetText(l, your_dataframe[1, names(l)])