Add labels to dendogram

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Add labels to dendogram

Luigi
Dear all,
I have built a hierarchical clustering on some data as follows:
```
Tag = c(
  "YP_008603282", "NP_054035",    "BAA00606",     "NP_054034",
 "NP_054033",
  "AAC17846" ,    "NP_054036",    "YP_073767" ,   "BAQ20411",     "P52455")
Healthy = c(
  12.15540751,  2.33103008,  1.46924258,  0.26274009,  0.95217008,
  -0.08197491,  0.09038259, -0.08197491, -0.25433241, -0.08197491)
Tumour = c(
  12.51939026,  1.20983671,  0.61459705,  0.61459705,  0.81301027,
  0.21777061,  -0.17905583, -0.17905583, -0.17905583,  0.01935739)
Metastasis = c(
  12.55328882,  1.04722513,  1.04722513,  0.70881149,  0.37039785,
  0.20119103, 0.20119103,    0.20119103,  0.20119103,  0.03198422)
df = data.frame(Tag, Healthy, Tumour, Metastasis, stringsAsFactors = FALSE)
d <- dist(df, method = "euclidean")
hc1 <- hclust(d, method = "complete" )
plot(hc1)
```

Is there a way to add the Tag column instead of the numbers to the leaves
of the dendrogram?
Thank you

--
Best regards,
Luigi

        [[alternative HTML version deleted]]

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Re: Add labels to dendogram

plangfelder
Your code does not work because Tag is not numeric. You need to exclude Tag
from the data frame df and instead assign it as rownames. Also, dist
requires a numeric matrix, not data frame.

df = as.matrix(data.frame(Healthy, Tumour, Metastasis))
or
df = cbind(Healthy, Tumour, Metastasis)

rownames(df) = Tag

Then continue as in your code.

Peter



On Thu, Mar 26, 2020 at 8:10 AM Luigi Marongiu <[hidden email]>
wrote:

> Dear all,
> I have built a hierarchical clustering on some data as follows:
> ```
> Tag = c(
>   "YP_008603282", "NP_054035",    "BAA00606",     "NP_054034",
>  "NP_054033",
>   "AAC17846" ,    "NP_054036",    "YP_073767" ,   "BAQ20411",     "P52455")
> Healthy = c(
>   12.15540751,  2.33103008,  1.46924258,  0.26274009,  0.95217008,
>   -0.08197491,  0.09038259, -0.08197491, -0.25433241, -0.08197491)
> Tumour = c(
>   12.51939026,  1.20983671,  0.61459705,  0.61459705,  0.81301027,
>   0.21777061,  -0.17905583, -0.17905583, -0.17905583,  0.01935739)
> Metastasis = c(
>   12.55328882,  1.04722513,  1.04722513,  0.70881149,  0.37039785,
>   0.20119103, 0.20119103,    0.20119103,  0.20119103,  0.03198422)
> df = data.frame(Tag, Healthy, Tumour, Metastasis, stringsAsFactors = FALSE)
> d <- dist(df, method = "euclidean")
> hc1 <- hclust(d, method = "complete" )
> plot(hc1)
> ```
>
> Is there a way to add the Tag column instead of the numbers to the leaves
> of the dendrogram?
> Thank you
>
> --
> Best regards,
> Luigi
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: Add labels to dendogram

Luigi
Thank you!

On Thu, Mar 26, 2020 at 5:07 PM Peter Langfelder <[hidden email]>
wrote:

> Your code does not work because Tag is not numeric. You need to exclude
> Tag from the data frame df and instead assign it as rownames. Also, dist
> requires a numeric matrix, not data frame.
>
> df = as.matrix(data.frame(Healthy, Tumour, Metastasis))
> or
> df = cbind(Healthy, Tumour, Metastasis)
>
> rownames(df) = Tag
>
> Then continue as in your code.
>
> Peter
>
>
>
> On Thu, Mar 26, 2020 at 8:10 AM Luigi Marongiu <[hidden email]>
> wrote:
>
>> Dear all,
>> I have built a hierarchical clustering on some data as follows:
>> ```
>> Tag = c(
>>   "YP_008603282", "NP_054035",    "BAA00606",     "NP_054034",
>>  "NP_054033",
>>   "AAC17846" ,    "NP_054036",    "YP_073767" ,   "BAQ20411",
>>  "P52455")
>> Healthy = c(
>>   12.15540751,  2.33103008,  1.46924258,  0.26274009,  0.95217008,
>>   -0.08197491,  0.09038259, -0.08197491, -0.25433241, -0.08197491)
>> Tumour = c(
>>   12.51939026,  1.20983671,  0.61459705,  0.61459705,  0.81301027,
>>   0.21777061,  -0.17905583, -0.17905583, -0.17905583,  0.01935739)
>> Metastasis = c(
>>   12.55328882,  1.04722513,  1.04722513,  0.70881149,  0.37039785,
>>   0.20119103, 0.20119103,    0.20119103,  0.20119103,  0.03198422)
>> df = data.frame(Tag, Healthy, Tumour, Metastasis, stringsAsFactors =
>> FALSE)
>> d <- dist(df, method = "euclidean")
>> hc1 <- hclust(d, method = "complete" )
>> plot(hc1)
>> ```
>>
>> Is there a way to add the Tag column instead of the numbers to the leaves
>> of the dendrogram?
>> Thank you
>>
>> --
>> Best regards,
>> Luigi
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>

--
Best regards,
Luigi

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.