I have a data that looks like this:
Cluster_Combined Cluster_1 Cluster_2 Cluster_3 Cluster_4 Cluster_6 Cluster_10
G-protein coupled receptor signaling pathway (15) 2 6 0 4 3 1 0
GTP catabolic process (69) 1 0 0 0 2 0 0
activin receptor signaling pathway (17) 0 2 0 0 0 0 0
acute inflammatory response (7) 2 1 0 0 1 0 0
acute-phase response (8) 5 2 1 0 2 0 0
aging (5) 2 1 2 0 1 0 1
Which I want to create the heat map, based on the values above, where columns refer to the cluster name and row the ontology terms.
Now I have the code below
library(gplots);
dat <- read.table("http://dpaste.com/1505883/plain/",sep="\t",header=T);
hmcols <- rev(redgreen(2750));
heatmap.2(as.matrix(dat),scale="row",cols=hmcols,trace="none",dendrogram="none",keysize=1);
Although it does generate the plot, it gave me the following error:
Error in csep + 0.5 : non-numeric argument to binary operator
Furthermore, I cannot see the red-green effect in the plot.
How can I remove the error?
There is no "cols=" argument to heatmap.2(...). Try col=hmcols.
heatmap.2(as.matrix(dat),scale="row",col=hmcols,trace="none",dendrogram="none",keysize=1)
Related
I am very new to R, so I apologise if this looks simple to someone.
I try to to join two files and then perform a one-sided Fisher's exact test to determine if there is a greater burden of qualifying variants in casefile or controlfile.
casefile:
GENE CASE_COUNT_HET CASE_COUNT_CH CASE_COUNT_HOM CASE_TOTAL_AC
ENSG00000124209 1 0 0 1
ENSG00000064703 1 1 0 9
ENSG00000171408 1 0 0 1
ENSG00000110514 1 1 1 12
ENSG00000247077 1 1 1 7
controlfile:
GENE CASE_COUNT_HET CASE_COUNT_CH CASE_COUNT_HOM CASE_TOTAL_AC
ENSG00000124209 1 0 0 1
ENSG00000064703 1 1 0 9
ENSG00000171408 1 0 0 1
ENSG00000110514 1 1 1 12
ENSG00000247077 1 1 1 7
ENSG00000174776 1 1 0 2
ENSG00000076864 1 0 1 13
ENSG00000086015 1 0 1 25
I have this script:
#!/usr/bin/env Rscript
library("argparse")
suppressPackageStartupMessages(library("argparse"))
parser <- ArgumentParser()
parser$add_argument("--casefile", action="store")
parser$add_argument("--casesize", action="store", type="integer")
parser$add_argument("--controlfile", action="store")
parser$add_argument("--controlsize", action="store", type="integer")
parser$add_argument("--outfile", action="store")
args <- parser$parse_args()
case.dat<-read.delim(args$casefile, header=T, stringsAsFactors=F, sep="\t")
names(case.dat)[1]<-"GENE"
control.dat<-read.delim(args$controlfile, header=T, stringsAsFactors=F, sep="\t")
names(control.dat)[1]<-"GENE"
dat<-merge(case.dat, control.dat, by="GENE", all.x=T, all.y=T)
dat[is.na(dat)]<-0
dat$P_DOM<-0
dat$P_REC<-0
for(i in 1:nrow(dat)){
#Dominant model
case_count<-dat[i,]$CASE_COUNT_HET+dat[i,]$CASE_COUNT_HOM
control_count<-dat[i,]$CONTROL_COUNT_HET+dat[i,]$CONTROL_COUNT_HOM
if(case_count>args$casesize){
case_count<-args$casesize
}else if(case_count<0){
case_count<-0
}
if(control_count>args$controlsize){
control_count<-args$controlsize
}else if(control_count<0){
control_count<-0
}
mat<-cbind(c(case_count, (args$casesize-case_count)), c(control_count, (args$controlsize-control_count)))
dat[i,]$P_DOM<-fisher.test(mat, alternative="greater")$p.value
and problem starts in here:
case_count<-dat[i,]$CASE_COUNT_HET+dat[i,]$CASE_COUNT_HOM
control_count<-dat[i,]$CONTROL_COUNT_HET+dat[i,]$CONTROL_COUNT_HOM
the result of case_count and control_count is NULL values, however corresponding columns in both input files are NOT empty.
I tried to run the script above with assigning absolute numbers (1000 and 2000) to variables case_count and control_count , and the script worked without issues.
The main purpose of the code:
https://github.com/mhguo1/TRAPD
Run burden testing This script will run the actual burden testing. It
performs a one-sided Fisher's exact test to determine if there is a
greater burden of qualifying variants in cases as compared to controls
for each gene. It will perform this burden testing under a dominant
and a recessive model.
It requires R; the script was tested using R v3.1, but any version of
R should work. The script should be run as: Rscript burden.R
--casefile casecounts.txt --casesize 100 --controlfile controlcounts.txt --controlsize 60000 --output burden.out.txt
The script has 5 required options:
--casefile: Path to the counts file for the cases, as generated in Step 2A
--casesize: Number of cases that were tested in Step 2A
--controlfile: Path to the counts file for the controls, as generated in Step 2B
--controlsize: Number of controls that were tested in Step 2B. If using ExAC or gnomAD, please refer to the respective documentation for
total sample size
--output: Output file path/name Output: A tab delimited file with 10 columns:
#GENE: Gene name CASE_COUNT_HET: Number of cases carrying heterozygous qualifying variants in a given gene CASE_COUNT_CH: Number of cases
carrying potentially compound heterozygous qualifying variants in a
given gene CASE_COUNT_HOM: Number of cases carrying homozygous
qualifying variants in a given gene. CASE_TOTAL_AC: Total AC for a
given gene. CONTROL_COUNT_HET: Approximate number of controls carrying
heterozygous qualifying variants in a given gene CONTROL_COUNT_HOM:
Number of controlss carrying homozygous qualifying variants in a given
gene. CONTROL_TOTAL_AC: Total AC for a given gene. P_DOM: p-value
under the dominant model. P_REC: p-value under the recessive model.
I try to run genetic variant burden test with vcf files and external gnomAD controls. I found this repo suitable and trying to fix bugs now in it.
as a newbie in R statistics, I will be happy about any suggestion. Thank you!
If you want all row in two file. You can use full join with by = "GENE" and suffix as you wish
library(dplyr)
z <- outer_join(case_file, control_file, by = "GENE", suffix = c(".CASE", ".CONTROL"))
GENE CASE_COUNT_HET.CASE CASE_COUNT_CH.CASE CASE_COUNT_HOM.CASE CASE_TOTAL_AC.CASE
1 ENSG00000124209 1 0 0 1
2 ENSG00000064703 1 1 0 9
3 ENSG00000171408 1 0 0 1
4 ENSG00000110514 1 1 1 12
5 ENSG00000247077 1 1 1 7
6 ENSG00000174776 NA NA NA NA
7 ENSG00000076864 NA NA NA NA
8 ENSG00000086015 NA NA NA NA
CASE_COUNT_HET.CONTROL CASE_COUNT_CH.CONTROL CASE_COUNT_HOM.CONTROL CASE_TOTAL_AC.CONTROL
1 1 0 0 1
2 1 1 0 9
3 1 0 0 1
4 1 1 1 12
5 1 1 1 7
6 1 1 0 2
7 1 0 1 13
8 1 0 1 25
If you want only GENE that are in both rows, use inner_join
z <- inner_join(case_file, control_file, by = "GENE", suffix = c(".CASE", ".CONTROL"))
GENE CASE_COUNT_HET.CASE CASE_COUNT_CH.CASE CASE_COUNT_HOM.CASE CASE_TOTAL_AC.CASE
1 ENSG00000124209 1 0 0 1
2 ENSG00000064703 1 1 0 9
3 ENSG00000171408 1 0 0 1
4 ENSG00000110514 1 1 1 12
5 ENSG00000247077 1 1 1 7
CASE_COUNT_HET.CONTROL CASE_COUNT_CH.CONTROL CASE_COUNT_HOM.CONTROL CASE_TOTAL_AC.CONTROL
1 1 0 0 1
2 1 1 0 9
3 1 0 0 1
4 1 1 1 12
5 1 1 1 7
My code,
tree_model<-tree(readmitted_bin~ num_medications_01,data = tree_trainData)
plot(tree_model)
where readmitted_bin is a factor of 0 and 1 and num_medications_01 is scaled between 0 and 1. I have included other variables that also return the following error:
Error in plot.tree(tree_model) : cannot plot singlenode tree
3.
stop("cannot plot singlenode tree")
2.
plot.tree(tree_model)
1.
plot(tree_model)
The dataframe:
n|readmitted_bin
|
num_medications_01
1 0 0.3375
2 0 0.2125
3 0 0.0875
4 1 0.2000
5 1 0.1875
6 1 0.1250
Any help is appreciated on how tree() works.
For my previous lines of code for making tables from column names, they successfully made short and dense matrices for me to readily process data from two questions (from survey results): (2nd example).
However, when I try using the same line of code (above), I don't get that sleek matrix. I end up getting a list of un-linked tables, which I do not want. Perhaps it's due to the new column only having 0's and 1's as numeric characters, vs. the others that have more than 2: (1st example).
[Please forgive my formatting issues (StackOverflow Status: Newbie). Also, many thanks in advance to those checking in on and answering my question!]
>table(select(data_final, `Relationship 2Affected Individual`, Satisfied_Treatments))
Relationship 2Affected Individual 1
1 0
2 0
3 0
6 0
Other (please specify) 0
, , 1 = 1, Response = 10679308122
0
Relationship 2Affected Individual 1
1 0
2 0
3 0
6 0
Other (please specify) 0
, ,
...
> table(select(data_final, `Relationship 2Affected Individual`, Indirect_Benefits))
Indirect_Benefits
Relationship 2Affected Individual 0 1 2 3
1 4 1 0 0
2 42 17 9 3
3 12 1 1 0
6 5 2 2 0
Other (please specify) 1 0 0 0
>#rstudioapi::versionInfo()
>#packageVersion("dplyr")
table(data_final$Relationship 2Affected Individual, data_final$Satisfied_Treatments)
Problem Solved^
In the vegan package, I tried to make a ordination plot with species as objects and environmental variables as vectors. However the environmental variables are regarded as centroids instead of factors. Strangely each data frame cell is seen as an environmental factor, so I think the dataframe is not structured correctly. When I plot the ordination without environmental variables I don't get any problems.
summary(gutter.dca)
environfit = envfit(gutter.dca,gutterenv)
> head(environfit)
$vectors
NULL
$factors
Centroids:
DCA1 DCA2
vocht0,246435845 -0.2185 -1.0601
vocht0,249249249 0.1932 -1.1339
vocht0,251497006 0.0331 -2.0888
vocht0,264735265 -0.3353 -1.3403
vocht0,26911315 -0.0017 -0.9498
vocht0,272369715 -1.0733 0.0021
Species dataframe
head(gutter)
Acer.campestre Acer.pseudoplantanus Adoxa.moschatellina Aegopodium.podagraria Ajuga.reptans
Q1-1 0 0 5 0 0
Q1-2 0 70 15 20 0
Q1-3 0 15 0 0 0
Q1-4 0 3 0 0 0
Q2-1 0 3 0 0 0
Q2-2 1 0 0 0 0
Environmental variables dataframe
head(gutterenv)
vocht Ph.H2O ph.KCl mg.NO3.kg.soil mg.NH4.N.kg.soil litter.depth..cm.
1 0,26911315 7,41 6,686 2,811031105 4,674304351 7,5
2 0,246435845 7,225 6,349 2,567981088 6,735395066 6,5
3 0,264735265 7,001 6,491 2,336821354 8,400116244 5,1
4 0,325123153 6,732 5,444 2,518858082 7,684506342 8,25
5 0,446875 6,87 7,45 2,443686352 9,886923756 4
6 0,548476454 8,1 7,05 3,144954614 11,3179919 3
I have a sample code in R as follows:
library(igraph)
rm(list=ls())
dat=read.csv(file.choose(),header=TRUE,row.names=1,check.names=T) # read .csv file
m=as.matrix(dat)
net=graph.adjacency(adjmatrix=m,mode="undirected",weighted=TRUE,diag=FALSE)
where I used csv file as input which contain following data:
23732 23778 23824 23871 58009 58098 58256
23732 0 8 0 1 0 10 0
23778 8 0 1 15 0 1 0
23824 0 1 0 0 0 0 0
23871 1 15 0 0 1 5 0
58009 0 0 0 1 0 7 0
58098 10 1 0 5 7 0 1
58256 0 0 0 0 0 1 0
After this I used following command to check weight values:
E(net)$weight
Expected output is somewhat like this:
> E(net)$weight
[1] 8 1 10 1 15 1 1 5 7 1
But I'm getting weird values (and every time different):
> E(net)$weight
[1] 2.121996e-314 2.121996e-313 1.697597e-313 1.291034e-57 1.273197e-312 5.092790e-313 2.121996e-314 2.121996e-314 6.320627e-316 2.121996e-314 1.273197e-312 2.121996e-313
[13] 8.026755e-316 9.734900e-72 1.273197e-312 8.027076e-316 6.320491e-316 8.190221e-316 5.092790e-313 1.968065e-62 6.358638e-316
I'm unable to find where and what I am doing wrong?
Please help me to get the correct expected result and also please tell me why is this weird output and that too every time different when I run it.??
Thanks,
Nitin
Just a small working example below, much clearer than CSV input.
library('igraph');
adjm1<-matrix(sample(0:1,100,replace=TRUE,prob=c(0.9,01)),nc=10);
g1<-graph.adjacency(adjm1);
plot(g1)
P.s. ?graph.adjacency has a lot of good examples (remember to run library('igraph')).
Related threads
Creating co-occurrence matrix
Co-occurrence matrix using SAC?
The problem seems to be due to the data-type of the matrix elements. graph.adjacency expects elements of type numeric. Not sure if its a bug.
After you do,
m <- as.matrix(dat)
set its mode to numeric by:
mode(m) <- "numeric"
And then do:
net <- graph.adjacency(m, mode = "undirected", weighted = TRUE, diag = FALSE)
> E(net)$weight
[1] 8 1 10 1 15 1 1 5 7 1