guokai8 / candihap Goto Github PK
View Code? Open in Web Editor NEWBuild haplotye and generate figures
License: GNU General Public License v3.0
Build haplotye and generate figures
License: GNU General Public License v3.0
hello Dr. Guo
I have a problem when I used snboxplot module in Candihap.
the error message is "Insufficient values in manual scale. 6 needed but only 4 provided". it seems something wrong which ggplot2 packages, but i dont know how to deal with this problem .
Hap_results <- results(hap, gene="Si9g49990")
if (! require("LDheatmap")) install.packages("LDheatmap")
if (! require("genetics")) install.packages("genetics")
LDsnp <- Hap_results[, !names(Hap_results) %in% c("sample","Info")]
LDsnp = LDsnp[,-ncol(LDsnp)]
NAs <- LDsnp == "N/N"
is.na(LDsnp)[NAs] <- TRUE
LDsnp[NAs] <- NA
LDsnp = LDsnp[-1,]
Dist = as.numeric(LDsnp[1,])
LDsnp = LDsnp[-c(1:6),]
num<-ncol(LDsnp)
for(i in 1:num){
LDsnp[,i]<-as.genotype(LDsnp[,i])
}
rgb.palette <- colorRampPalette(rev(c("#1F77B4", "#AEC7E8", "#FF7F0E")), space = "rgb")
LDheatmap(LDsnp, genetic.distances = Dist, flip = TRUE, color=rgb.palette(40))
Dear CandiHap team:
Is the CandiHap software no longer supported on windows_X64? Thank you very much
The function snp2hap exit with the following error:
Error in gr[x][, c("REF", "ALT", hapind[[x]])] :
'j' cannot mix between and within metadata column names
The command is as follows:
my.hap <- snp2hap(my.pheno,my.ovl)
The object my.pheno is:
my.pheno
sample test
1 WB-001 1
2 WB-002 2
3 WB-003 3
4 WB-004 4
5 WB-005 5
6 WB-006 6
7 WB-007 7
8 WB-008 8
9 WB-009 9
10 WB-010 10
while the object my.ovl was created with the followinf two functions:
my.hmp <-read_hmp("haplotypes.hmp", comment = "&")
my.ovl <- findover(my.gr,my.hmp)
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.