[R] Change font size in Cluster analysis
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Jun 27 13:01:46 CEST 2013
Your example is not reproducible (see the posting guide), but using
example(hclust)
hc <- hclust(dist(USArrests), "ave")
plot(hc)
plot(hc, cex = 0.3)
the second has much smaller case names.
On 27/06/2013 11:12, Gitte Brinch Andersen wrote:
> Hello
>
> I have done a cluster analysis, and I would like to change the font size of my sample names. I have tried using cex, but this doesn't work/change anything. I have tried to specify it with cex.main, cex.lab, cex.axis and cex.sub, and can change all other names in the picture but my sample names.
> I can't see what I am doing wrong.
>
> I hope somebody can help me, and I apologize for this probably very simple question/mistake.
>
> I have around 1000 rows and 50 columns, but have only included a few in my example.
>
> Thank you in advance!
>
> Kind regards
>
> Gitte Andersen
>
>
> #Read in data
> data<-read.table("/Users/gban/Desktop/Heatmap/Heatmap with selected genes/Probes_for_heatmap_35_meth_diff_both_hypo_and_hypermeth_Gene&probenames.txt",sep="\t",dec=",",header=TRUE,row.names=1)
>
> data
> OS_Tumor1_08_14985_2_3 OS_Tumor2_08_226869_1
> CHST3_cg04268405_1 0.95038060 0.76433753
> DLX5_cg19962750_2 0.93111825 0.75384523
> ZIC4_cg12892506_3 0.86033747 0.69614933
> DLX5_cg05597836_4 0.90698171 0.66414891
>
>
>
> #Turn the data into a matrix, and transpose to get the columns to be clustered
> Data_matrix<-as.matrix(t(data))
>
> Data_matrix
> CHST3_cg04268405_1 DLX5_cg19962750_2
> OS_Tumor1_08_14985_2_3 0.9503806 0.9311183
> OS_Tumor2_08_226869_1 0.7643375 0.7538452
> OS_Tumor3_10_201917_2_3 0.7109182 0.7778035
> OS_Tumor4_00_2395 0.7772400 0.6769241
> OS_Tumor5_02_2669 0.9638739 0.9023436
> OS_Tumor6_02_4738 0.9028490 0.9586764
> OS_Tumor7_02_4850 0.8786524 0.8872261
> OS_Tumor8_02_6935 0.8434550 0.7180251
> OS_Tumor9_03_1430 0.7494400 0.9190213
> OS_Tumor10_03_1701 0.9148253 0.7692125
> OS_Tumor11_03_220 0.9270112 0.8607459
> OS_Tumor12_03_2558 0.9344832 0.5013390
> OS_Tumor13_03_373 0.9549153 0.9559071
> OS_Tumor14_03_82 0.9117558 0.3993953
> OS_Tumor15_06_22319 0.9580999 0.9645215
> OS_Tumor16_07_16581 0.6213243 0.9033265
> OS_Tumor17_07_28523 0.9064597 0.4421651
> OS_Tumor18_07_3212 0.6439032 0.4344106
> OS_Tumor19_07_6990 0.9350585 0.9238712
> OS_Tumor20_07_6990sample2 0.9526839 0.9027684
> OS_Tumor21_07_7724 0.9338156 0.8335415
> OS_Tumor22_08_10238 0.9028336 0.8529122
> OS_Tumor23_08_14985Sample2 0.9609952 0.9478541
> OS_Tumor24_08_16592 0.9168102 0.9138002
> OS_Tumor25_08_21197 0.9148711 0.9109843
> OS_Tumor26_08_21197Sample2 0.9583610 0.8830407
> OS_Tumor27_08_222863 0.9478853 0.8395278
> OS_Tumor28_08_225814 0.9451414 0.9407933
> OS_Tumor29_08_226869Sample2 0.9028336 0.8337000
> OS_Tumor30_08_230660 0.9599117 0.9363075
> OS_Tumor31_08_4485 0.8247909 0.8336728
> OS_Tumor32_09_214654 0.9531564 0.8957473
> OS_Tumor33_09_214654Sample2 0.9552210 0.9034464
> OS_Tumor34_10_200150 0.9332627 0.8551589
> OS_Tumor35_10_201917 0.9397219 0.9470733
> OS_Tumor36_10_201917Sample2 0.9607446 0.9523402
> OS_Tumor37_10_202221 0.9264254 0.9413189
> OS_Tumor38_10_204294 0.8388658 0.8956207
> OS_Tumor39_10_204294Sample2 0.8071109 0.8474199
> OS_Tumor40_10_205933 0.8788835 0.4950936
> OS_Tumor41_10_225662 0.9334545 0.8910134
> OS_Tumor42_10_229129 0.5872184 0.8394597
> OS_Tumor43_11_236261 0.9015548 0.9293858
> OS_Tumor44_12_211561 0.6793692 0.1856015
> Normalbone.3. 0.1636323 0.1222070
> Normalbone.UA. 0.1934500 0.1303734
> Normalbone.UA2. 0.1737224 0.1604758
> CRL_11372 0.9779593 0.2533844
> CRL_1427 0.9598825 0.8862426
> CRL_1543 0.9283976 0.7198934
> CRL_2098 0.9325895 0.6360936
> Ho_f.4610 0.9370865 0.6279557
> HTB_85 0.9441092 0.1037401
> HTB_96 0.9511175 0.9160013
> ZIC4_cg12892506_3 DLX5_cg05597836_4
> OS_Tumor1_08_14985_2_3 0.86033747 0.90698171
> OS_Tumor2_08_226869_1 0.69614933 0.66414891
> OS_Tumor3_10_201917_2_3 0.58728927 0.65086446
> OS_Tumor4_00_2395 0.41747130 0.45464648
> OS_Tumor5_02_2669 0.74259213 0.88244165
> OS_Tumor6_02_4738 0.79690018 0.93691928
> OS_Tumor7_02_4850 0.05513471 0.91753824
> OS_Tumor8_02_6935 0.70742299 0.77802530
> OS_Tumor9_03_1430 0.84563086 0.87202952
> OS_Tumor10_03_1701 0.81318017 0.72446802
> OS_Tumor11_03_220 0.72489087 0.80580733
> OS_Tumor12_03_2558 0.06656780 0.14739011
> OS_Tumor13_03_373 0.94011867 0.95742989
> OS_Tumor14_03_82 0.52129769 0.54734874
> OS_Tumor15_06_22319 0.93025191 0.94392535
> OS_Tumor16_07_16581 0.67236887 0.88546907
> OS_Tumor17_07_28523 0.25764851 0.45550666
> OS_Tumor18_07_3212 0.33624514 0.18623351
> OS_Tumor19_07_6990 0.82904776 0.88946081
> OS_Tumor20_07_6990sample2 0.76836030 0.82519665
> OS_Tumor21_07_7724 0.90314315 0.71810973
> OS_Tumor22_08_10238 0.83715782 0.86426252
> OS_Tumor23_08_14985Sample2 0.82588214 0.90655043
> OS_Tumor24_08_16592 0.77582828 0.83500490
> OS_Tumor25_08_21197 0.90274785 0.96119490
> OS_Tumor26_08_21197Sample2 0.87385578 0.83341529
> OS_Tumor27_08_222863 0.72588195 0.59849569
> OS_Tumor28_08_225814 0.87931232 0.89657489
> OS_Tumor29_08_226869Sample2 0.86379063 0.88825605
> OS_Tumor30_08_230660 0.92495563 0.95137547
> OS_Tumor31_08_4485 0.84465179 0.66948504
> OS_Tumor32_09_214654 0.92036441 0.71915709
> OS_Tumor33_09_214654Sample2 0.93955431 0.46490552
> OS_Tumor34_10_200150 0.80337813 0.82519665
> OS_Tumor35_10_201917 0.87734686 0.91265824
> OS_Tumor36_10_201917Sample2 0.93627004 0.94319232
> OS_Tumor37_10_202221 0.93107776 0.96075927
> OS_Tumor38_10_204294 0.85892154 0.94595920
> OS_Tumor39_10_204294Sample2 0.69839075 0.76396555
> OS_Tumor40_10_205933 0.25850129 0.43418918
> OS_Tumor41_10_225662 0.71442683 0.88154146
> OS_Tumor42_10_229129 0.42328977 0.77763541
> OS_Tumor43_11_236261 0.82946721 0.87242385
> OS_Tumor44_12_211561 0.84785994 0.12366988
> Normalbone.3. 0.06840225 0.08229536
> Normalbone.UA. 0.07383344 0.12502117
> Normalbone.UA2. 0.07741817 0.09563505
> CRL_11372 0.05409689 0.13815797
> CRL_1427 0.91730069 0.92421230
> CRL_1543 0.77789918 0.94650563
> CRL_2098 0.91524115 0.50725942
> Ho_f.4610 0.05736418 0.51843963
> HTB_85 0.95464468 0.05260867
> HTB_96 0.88410529 0.92872206
>
>
> #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: gitteba at hum-gen.au.dk<mailto:gitteba at hum-gen.au.dk>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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