Hello everyone,

I'm creating a heatmap with complexHeatmap and wonder how the distance calculation is done. It isn't a z-score because the values are going from 0-0.4 and I coudln't found information about the used  "get_dist(submat, distance)" function.

Thanks for any answer and/or helpful websites which explain how the distance is calculated ;)

CHeers

Annkatrin

.. never mind - it was my stupi mistake.. I didn't scale the matrix - that was the reason why the annotation label differs

Dear annkatrin,

your question is a bit confusing--- what do you mean about "how the distance calculation is done " ? 

Also, which exact code you used from the package ? 

If you type ?Heatmap, you can actually see all the available arguments and possible methodologies implemented, such as

clustering_distance_rows & clustering_distance_columns, which show by default that "euclidean Distance" is used.

Also, by default the ComplexHeatmap package (as far as i remember) does not perform any kind of scaling, so if you want you have to scale your data prior import to Heatmap().

You should anyway check the below vignette:

https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html

Best,

Efstathios

Hey Efstathios,

you are write - I ask my question very unclear ;) I am not curious about the clustering - sorry for the misunderstanding! I am curious about the created legend of Heatmap. 

E.g.:

if I run "heatmap.2(data_mat)": the legend ("Color Key and Histogram") goes from 0-1 and represent the range of data in my input file

if I run "heatmap.2(data_mat, trace="none", distfun=dist.pear, hclustfun=hclust.ave,scale="row", zlim=c(0,1))" : this legend represents the z-score of my data set

if I run "Heatmap(data_mat)": then I get a legend with a range from 0 till 0.4 and that's what I don't understand - how is this calculated?

I hope that's better to understand ;)