How to remove individual attributes within cluster plots

Question

I would like a fairly plain, publication-quality cluster plot. I have created the plot and removed the title, legend and adjusted the axis titles, with the script provided. However, I would also like to remove all of the individual row labels 'attributes' that are my sample ID's within each of the two cluster's e.g. CLR45, HTR132. Is this possible?

fviz_cluster(k2, data = Chem)+ theme(legend.position = "none")+labs(title = "") +  theme(
        axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")),
        axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm")))

dput(head(Chem,50))
structure(c(0.147411356827536, -0.94833184269442, -0.236098761737746, 
-0.156408346996621, -1.07782876612066, 0.15737266025443, -0.85369947703763, 
-0.684357344128487, -0.744125156240499, -0.166369650423515, 1.06883177595158, 
-1.72531338325188, -1.16249983257523, -0.908486633211519, -1.30693870691714, 
-1.04296420835121, 0.336676092365792, -0.45026675161856, -0.455247403332007, 
-0.935222767283235, -0.798912316639064, 0.185622913832727, -0.345812539076084, 
0.264855107585394, -0.649213869051943, -0.745838498773852, -0.952615203252478, 
0.510998876988382, 1.40751604176986, -0.749105803729271, 0.222121124079889, 
0.146973059409158, -0.25104071265341, -0.176330949625734, -0.734163852813605, 
1.1584834941196, 0.869605741211104, 0.202198517226101, 0.301811538821014, 
-0.0567953296263845, -0.669415393212821, -0.191272904766074, 
-0.71922190189794, 0.222121124079889, -0.51999586293279, -0.231118110024299, 
0.5608053856735, -0.285905270422864, -0.614628232814256, 0.0378370402550813, 
1.21148988263212, -0.722729092058211, 0.938866964062205, 1.29275958711264, 
1.23956487191698, 1.86977449177269, 1.84761002727152, 2.09068032585176, 
0.430561900436177, -0.339283848035902, 3.19668712695198, -0.305298335931744, 
-0.0186379222283033, 3.76926913851535, -0.987963856121806, 0.356680351444172, 
3.44123505721924, 0.255462628028634, -1.00052371956831, -0.425184448439876, 
-0.0334142322231424, -0.313100227585446, -1.0460909046001, 0.779075947446034, 
-1.04523092273039, -0.432924280356334, -0.788096532267007, 0.836910424803157, 
0.471935569011041, -0.841678386878241, 3.4264587472244, 0.770476135624245, 
1.97394747659788, 0.635952609659098, -0.86162640581326, -0.502562073822641, 
0.695796664499772, -0.659190958982183, 0.126169915328244, -0.127243800150166, 
-0.945851372685624, -0.589742302104659, -0.506994966919312, -0.665840298627189, 
-0.90004481199628, -0.82320799963024, -0.566839021759986, -0.759669866554213, 
-0.980575700633291, 0.208917251495781, -1.23882313589815, -0.816688277463794, 
0.346387764578252, 0.524062438145321, 1.46662027130976, -0.917496601945682, 
1.0860688452788, 2.10423292402831, 0.254400170526879, -0.804087236829436, 
-0.843150462529107, -0.300045614716482, 0.672754716385498, -0.9527795153661, 
-0.622632253058524, 0.0175006072532231, 0.578246912369032, 1.71864108103204, 
-1.24512365636358, 2.67546329317061, -1.0435070073998, -1.24421134102627, 
1.42382713735224, 2.28432699595981, 0.587773297320356, 0.00106885031820219, 
0.211304610661984, -0.589869547527789, 0.65259305148912, 0.00867987889811877, 
-1.54754862951275, 0.235750629237659, -0.331548216154132, 1.18561706626058, 
-0.368091233667634, -1.09769148192, -1.03846659132395, -0.70957943281297, 
-0.316426967333605, -1.05358783984799, -1.19471949412263, -0.788965988305396, 
0.663933988919855, 0.346387764578252, 0.137210492538405, 0.146031220893509, 
-0.456298517515165, -0.534424969210994, 0.450976402525343, 0.193915175837746, 
1.53543257619906, -0.518118831649496, -0.16974850422888, 0.380309904408398, 
-0.518118831649496, -0.114742659464473, 3.20394309995186, 1.0953858473389, 
0.893697766122234, 0.710344953491444, -0.316430750432833, 0.453651027510375, 
-0.444777708547519, 1.99381459314849, -0.664801077853449, 1.99381459314849, 
0.343639347733259, 0.105280700089759, -0.811483324057402, 3.43885470777859, 
-0.829818602394972, 0.948923628687728, -1.17727227024187, 0.507850124084635, 
-0.054162900383238, 0.0383202589981529, -0.111075611598317, 0.215292379866875, 
-0.243089627330857, -0.609795233089042, -0.499783553311926, -0.367182807190326, 
-0.719806922617856, 0.105280700089759, -0.353101307107973, 0.728680241580711, 
-0.848153880732542, -0.994836126936495, -1.26986533125513, -0.976500848598925, 
0.398645192497665, -1.01317140527406, 0.123615978427329, -0.774812757630565, 
-1.08651252837604, -0.646465799515879, -0.536454109987066, -0.829818602394972, 
0.508656872274782, -0.518118831649496, 0.675002376238412, -0.0617082448613822, 
-0.668996727923662, -1.60481832778947, -0.71877447345135, 0.625224632383091, 
-1.78899598306442, -0.793441090906698, -1.09210755738336, 1.32211305639179, 
-1.96321808990278, -1.51521838684306, 0.00549171084843096, -2.9911285157337, 
0.276780418706376, -2.1225068715777, -1.56499613237074, -0.683930051414732, 
0.271802645324263, 0.398636337390084, -0.270774772063992, 0.662607717406351, 
1.26287754043467, -0.00695272427921605, 0.459290519580567, -0.0828886740640689, 
-0.779976209944577, 0.525669143000081, 1.64566839646848, -0.527130156430866, 
-1.99806251026703, 0.852509813910332, -1.05477425032805, 0.0726916665582448, 
0.177224929323366, 0.824335611149109, -0.444996877229983, -0.0218860477702858, 
-1.2713074392762, -0.270774772063992, -0.0467749213703124, 0.625224632383091, 
-0.569441240213019, 0.722291233402677, 0.401224781689411, 0.127447185468045, 
0.80442451260356, -0.594330112140679, 0.824335611149109, 0.276780418706376
), .Dim = c(50L, 5L), .Dimnames = list(c("CLR16", "CLR36", "CLR52", 
"CLR56", "CLR20", "CLR22", "CLR11", "CLR14", "CLR17", "CLR33", 
"CLR41", "CLR43", "CLR50", "CLR32", "CLR35", "CLR37", "CLR45", 
"CLR48", "CLR49", "CLR5", "CLR55", "CLR58", "CLR59", "CLR6", 
"CLR60", "CLR61", "CLR62", "CLR65", "CLR66", "CLR67", "CLR68", 
"CLR7", "GGR70", "GGR77", "GGR71", "GGR69", "GGR72", "GGR73", 
"GGR74", "GGR75", "GGR76", "GGR78", "GGR79", "GGR80", "GGR81", 
"GGR83", "GGR84", "GGR85", "GGR87", "GGR89"), c("X88Sr_umol_molCa", 
"X138Ba_umol_molCa", "X25Mg_umol_molCa", "X55Mn_umol_molCa", 
"X7Li_umol_molCa")))

UseR10085 · Accepted Answer · 2020-10-09T06:43:49.450

1

You can use labelsize = 0 as shown in the following code

library("factoextra")

# Data preparation
data("iris")
head(iris)
# Remove species column (5) and scale the data
iris.scaled <- scale(iris[, -5])

# K-means clustering
km.res <- kmeans(iris.scaled, 3, nstart = 25)

# Visualize kmeans clustering
fviz_cluster(km.res, iris[, -5], labelsize = 0) + 
  theme(legend.position = "none") + labs(title = "") +  
  theme(axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")),
  axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm")))

To remove all the little geometric shapes use geom = NULL like

fviz_cluster(km.res, iris[, -5], geom = NULL, labelsize = 0) + 
  theme(legend.position = "none") + labs(title = "") +  
  theme(axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")),
  axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm")))

To remove cluster centers use show.clust.cent = F

fviz_cluster(km.res, iris[, -5], geom = NULL, labelsize = 0, show.clust.cent = F) + 
  theme(legend.position = "none") + labs(title = "") +  
  theme(axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")),
  axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm")))

edited Oct 09 '20 at 06:43

answered Oct 09 '20 at 06:18

UseR10085

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Thankyou. Is it possible to remove all of the little geometric shapes as well so the cluster's are just a solid colour. I intend to include a table of the proportions of each of my locations that fall into the clusters – Angela Oct 09 '20 at 06:25
fviz_cluster(k2, data = Chem), labelsize = 0) + theme(legend.position = "none")+labs(title = "") + theme( axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")), axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm"))) – Angela Oct 09 '20 at 06:30
Have I done this wrong because I got an error : Error: unexpected ',' in "fviz_cluster(k2, data = Chem)," – Angela Oct 09 '20 at 06:31
Can you provide your data as `dput(Chem)`? – UseR10085 Oct 09 '20 at 06:32
This worked: fviz_cluster(k2, data = Chem, geom = NULL, labelsize = 0) + theme(legend.position = "none")+labs(title = "") + theme( axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")), axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm"))) – Angela Oct 09 '20 at 06:34
That worked except that, and this is being pedantic, but if you look closely in the pink cluster there is one small dot left over. Do you know why this would remain? – Angela Oct 09 '20 at 06:39
dput(Chem)fviz_cluster(k2, data = Chem, geom = NULL, labelsize = 0) + theme(legend.position = "none")+labs(title = "") + theme( axis.title.x = element_text(margin = unit(c(3, 0, 0, 0), "mm")), axis.title.y = element_text(margin = unit(c(0, 3, 0, 0), "mm"))) – Angela Oct 09 '20 at 06:40
Is this how I provide my data? – Angela Oct 09 '20 at 06:40
Run `dput(Chem)` in R and edit your question by copy and pasting the output of `dput()`. For details visit [How to make a great R reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). See my updated answer. Don't forget to [accept](https://stackoverflow.com/help/someone-answers) it. – UseR10085 Oct 09 '20 at 06:42
Actually, I just noticed your 'clean' cluster plot has the dot remaining as well in the pink cluster – Angela Oct 09 '20 at 06:45
My data is very long is there a way to provide a reduced data set? Also I can't see the check box I am supposed to tick to accept the answer. Sorry I'm a new to this – Angela Oct 09 '20 at 06:58
Use `dput(head(Chem, 50)`. Don't understand `I can't see the check box`, Can you show the desired output by editing the question? It was not part of your initial question. – UseR10085 Oct 09 '20 at 07:00
To accept an answer: Choose one answer that you believe is the best solution to your problem. To mark an answer as accepted, click on the check mark beside the answer to toggle it from greyed out to filled in. – Angela Oct 09 '20 at 08:12
Below the inverted triangle (upvote downvote), click on this √ to accept the answer. – UseR10085 Oct 09 '20 at 09:22
Sorry for the delay Bappa Das. I have just edited my initial question with the output from dput(head(Chem,50) – Angela Oct 14 '20 at 00:12

How to remove individual attributes within cluster plots

1 Answers1