[R] Space in label name
Hi
I am doing a cluster analysis and I have some troubles with the label names.
In the text file I have my data in, the first row contains the names of the
samples. They are called "FFPE Tumor 2", "Fresh Frozen Tumor 2" etc.
But when the cluster is made the label names contains periods instead of space
in the name.
I can't figure out how to change this, so I get spaces in the label names.
I hope someone can help?
The code I have used is:
#Set where you want to save your images/clusters
setwd("/Users/gban/Desktop/Lung Cancer/PAXgene article figures/PAXgene cluster
+ Venn analysis")
#Read in data
data<-read.table("/Users/gban/Desktop/Lung Cancer/PAXgene article
figures/PAXgene cluster + Venn
analysis/BetaValue_ALL_tumo1_dup2_Codename.txt",sep="\t",dec=",",header=TRUE)
# Throw out rows with missing values.
data = na.omit(data)
#Turn the data into a matrix
Data_matrix<-as.matrix(data)
#Calculate the distance
Data_dist<-dist(t(data))
#Make the cluster
hc = hclust(Data_dist,method="ward")
# reduced label size
par(cex=0.7, mar=c(5, 8, 4, 1))
plot(hc, xlab="", ylab="", main="", sub="", axes=FALSE)
par(cex=1)
title(xlab="", ylab="", main="Cluster analysis")
axis(2)
The cluster output:
[cid:D57BB82B-3ACF-4681-BCA8-D8202EA34294@eduroam.net.au.dk]
Kind regards
Gitte Brinch Andersen
Ph.d student
Department of Biomedicine
Wilhelm Meyers Allé 4
Aarhus Universitet
DK-8000 Aarhus C
E-mail: gitt...@hum-gen.au.dk<mailto:gitt...@hum-gen.au.dk>
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[R] Change font size in Cluster analysis
36_4 OS_Tumor1_08_14985_2_3 0.860337470.90698171 OS_Tumor2_08_226869_1 0.696149330.66414891 OS_Tumor3_10_201917_2_30.587289270.65086446 OS_Tumor4_00_2395 0.417471300.45464648 OS_Tumor5_02_2669 0.742592130.88244165 OS_Tumor6_02_4738 0.796900180.93691928 OS_Tumor7_02_4850 0.055134710.91753824 OS_Tumor8_02_6935 0.707422990.77802530 OS_Tumor9_03_1430 0.845630860.87202952 OS_Tumor10_03_1701 0.813180170.72446802 OS_Tumor11_03_220 0.724890870.80580733 OS_Tumor12_03_2558 0.066567800.14739011 OS_Tumor13_03_373 0.940118670.95742989 OS_Tumor14_03_82 0.521297690.54734874 OS_Tumor15_06_223190.930251910.94392535 OS_Tumor16_07_165810.672368870.88546907 OS_Tumor17_07_285230.257648510.45550666 OS_Tumor18_07_3212 0.336245140.18623351 OS_Tumor19_07_6990 0.829047760.88946081 OS_Tumor20_07_6990sample2 0.768360300.82519665 OS_Tumor21_07_7724 0.903143150.71810973 OS_Tumor22_08_102380.837157820.86426252 OS_Tumor23_08_14985Sample2 0.825882140.90655043 OS_Tumor24_08_165920.775828280.83500490 OS_Tumor25_08_211970.902747850.96119490 OS_Tumor26_08_21197Sample2 0.873855780.83341529 OS_Tumor27_08_222863 0.725881950.59849569 OS_Tumor28_08_225814 0.879312320.89657489 OS_Tumor29_08_226869Sample20.863790630.88825605 OS_Tumor30_08_230660 0.924955630.95137547 OS_Tumor31_08_4485 0.844651790.66948504 OS_Tumor32_09_214654 0.920364410.71915709 OS_Tumor33_09_214654Sample20.939554310.46490552 OS_Tumor34_10_200150 0.803378130.82519665 OS_Tumor35_10_201917 0.877346860.91265824 OS_Tumor36_10_201917Sample20.936270040.94319232 OS_Tumor37_10_202221 0.931077760.96075927 OS_Tumor38_10_204294 0.858921540.94595920 OS_Tumor39_10_204294Sample20.698390750.76396555 OS_Tumor40_10_205933 0.258501290.43418918 OS_Tumor41_10_225662 0.714426830.88154146 OS_Tumor42_10_229129 0.423289770.77763541 OS_Tumor43_11_236261 0.829467210.87242385 OS_Tumor44_12_211561 0.847859940.12366988 Normalbone.3. 0.068402250.08229536 Normalbone.UA. 0.073833440.12502117 Normalbone.UA2.0.077418170.09563505 CRL_11372 0.054096890.13815797 CRL_1427 0.917300690.92421230 CRL_1543 0.777899180.94650563 CRL_2098 0.915241150.50725942 Ho_f.4610 0.057364180.51843963 HTB_85 0.954644680.05260867 HTB_96 0.884105290.92872206 #Calculate the distance Data_dist<-dist(Data_matrix) #Make the cluster Data_clust<-hclust(Data_dist,method="ward") #Save the plot as a pdf file pdf(file="Cluster_Probes_From_genes_morethan_2_probes_and_morethan_30_methdiff.pdf") #Plot the cluster plot(Data_clust, cex=0.5) dev.off() #Ends the pdf saving. Gitte Brinch Andersen Kandidat-Ph.d. studerende Biomedicinsk Institut Wilhelm Meyers Allé 4 Aarhus Universitet DK-8000 Aarhus C Mobil: +45 30433317 E-mail: gitt...@hum-gen.au.dk<mailto:gitt...@hum-gen.au.dk> [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Heatmap with error message: `x' must be a numeric matrix
49332" DLX5_cg05597836_4 "0,906981714" "0,664148911" ARHGEF7_cg09129334_6 "0,88102921" "0,726231077" ZIC4_cg02387803_7 "0,770987986" "0,568085839" ZIC4_cg05855917_8 "0,880514891" "0,681148663" DLX5_cg13286614_9 "0,855132688" "0,592368469" ZIC4_cg04556126_10"0,907405655" "0,718858033" LOC145845_cg25718467_11 "0,893492688" "0,793191968" ZIC4_cg08393041_12"0,911133787" "0,678042743" SNED1_cg03785076_13 "0,862060883" "0,70294155" C10orf116_cg01004363_14 "0,858555164" "0,553920222" DLX5_cg20250426_15"0,903165828" "0,64976206" EPHX3_cg16184495_16 "0,927538308" "0,519523714" SNED1_cg21304158_17 "0,762270611" "0,647588457" EN1_cg12418535_19 "0,790529679" "0,318880892" RTKN_cg00689340_20"0,941714187" "0,675243565" SNED1_cg16937168_21 "0,894421593" "0,821448724" CD93_cg12873119_22"0,86949625" "0,676389091" RRN3P2_cg00525931_23 "0,862670615" "0,855822961" GPBAR1_cg18581950_24 "0,800216557" "0,810012301" SPARCL1_cg15552249_25 "0,815666773" "0,837099021" HOXD12_cg23130254_26 "0,840109076" "0,502896181" ZIC4_cg08889797_27"0,779606392" "0,591615859" ESRP2_cg06723863_28 "0,655488067" "0,47819514" ZIC4_cg16790847_29"0,735676228" "0,611372155" PFDN5_cg16309127_30 "0,753348167" "0,630504254" ARHGEF7_cg05776861_31 "0,951737748" "0,926613919" TBX15_cg24720355_32 "0,906521431" "0,364984479" FER1L5_cg01876130_33 "0,601084686" "0,805388591" HOXD12_cg1804_34 "0,865974739" "0,543178066" DLX6AS_cg26251506_35 "0,804479354" "0,538022928" GSTM5_cg05376982_36 "0,733426641" "0,552089202" ZIC4_cg12976081_37"0,464939006" "0,551218578" HOXB4_cg02132714_38 "0,798491712" "0,718121432" HOXD10_cg17489939_39 "0,970868858" "0,790134913" C10orf116_cg12261786_40 "0,727394677" "0,573072856" SPARCL1_cg19466563_41 "0,79754226" "0,722582785" HOXD12_cg03964958_42 "0,778450531" "0,679889139" HOXA5_cg09549073_43 "0,4652904""0,377825589" ZIC4_cg00334063_44"0,783052842" "0,634682328" TBX15_cg16990168_45 "0,893463329" "0,235197972" heatmap.2(data1, col=redgreen(75), scale="row", key=T, keysize=1.5,density.info="none", trace="none",cexCol=0.9, labRow=NA) Fejl i heatmap.2(data1, col = redgreen(75), scale = "row", key = T, : `x' must be a numeric matrix Many thanks! Kind regards Gitte Brinch Andersen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing package
Hi
I am trying to install a package (bioconductor) but every time I try to install
it I get this message:
source("http://bioconductor.org/biocLite.R";)
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
'lib = "C:/Program Files/R/R-3.0.0/library"' is not writable
Error in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
unable to install packages
> biocLite("methylumi")
I normally use mac computers, but I cannot get the right path for the folders I
should use, so now I am trying with a windows platform instead. But now I
cannot install one of the packages my pipeline needs.
Can anyone help?
I know it is probably a simple problem, but I have never used R before and
don't know how to solve problems in it.
Best
Gitte Andersen
E-mail: gitt...@hum-gen.au.dk
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] R cannot find the path on my mac
Hi
I am really sorry for this probably quite simple question.
I am new to R, and I am running a pipeline that has already been made. All I
have to do is give the paths for different folders, where the pipeline can find
the files with my data.
But every time I try to run the pipeline it returns with the message, that it
cannot find the file. And I really don't know why. I have found the path by
going to the folder and finding the info about the folder, where the location
of this is stated. I copy-paste this into the source command.
The path for the folder is:
When found with the "info about the folder":
/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis
But I think it should be:
/Users/gban/Desktop/Methylation
analysis/MethylationDataAnalysis/1.Normalization_raw_data/
as it is the folder 1.Normalization_raw_data where my data are in.
I have tried both paths but it returns with this message every time:
> source('/Users/gban/Desktop/Methylation
> analysis/MethylationDataAnalysis/1.Normalization_raw_data/pipelineIlluminaMethylation.main.R')
Fejl i file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Advarselsbesked:
In file(filename, "r", encoding = encoding) :
cannot open file '/Users/gban/Desktop/Methylation
analysis/MethylationDataAnalysis/1.
450K_pipeline_Nov2012release./SRC/loadMethylumi2.R': No such file or directory
Do you have any idea why?
I know this is probably more a question of how to type the path on a mac, than
it is a question of how R works.
But I am really frustrated about this, and thought it might be possible for you
to help?
Thank you in advance, and again sorry for the quite stupid question.
Best
Gitte Brinch Andersen
E-mail: gitt...@hum-gen.au.dk
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
