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Questions tagged [heatmaply]

heatmaply is an actively maintained open-source heatmap package for R, based upon the plotly R and JavaScript libraries.

heatmaply is an actively maintained heatmap visualisation package based on the plotly R and JavaScript libraries.

Bug reports can be filed at the project's github page.

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Is it possible to change the order of columns in heatmaply?

I have created a dendrogram with heatmaply with a dendrogram object from the dendextend package. I was wondering if there is a way to change the order of the columns: vs, am, carb, wt, drat, gear, etc. For example, I want to sort them…
Sara Altamirano
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Add mean values of the columns of the Heatmaply heatmap as an anotation near it

How can I add the mean values of the columns of the Heatmaply heatmap as an anotation near it? Currently, as a not ideal approach, I run this and got the below figure: x<- mtcars mmeans <-round(rowMeans(mtcars), digits = 2 ) rownames(x) <-…
entropy
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R - using heatmaply for a 2d histogram / density

I'm rather new to programming and the site so let me know if I screw up on this explanation. I have a rather long series of x, y coordinates representing a character in 2d space. Let's say that space is 200 x 400. I want to represent the amount of…
Sfawas
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Clustering in pheatmap and heatmaply R packages

I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same clustering (ordering of rows and columns) I get using the pheatmap package. Therefore, I would like the two commands to…
Arturo
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Association Clusters to Heatmap

I have two seperate dataframes, from one of these I have already created a heatmap from the first dataframe, however I want to add a sidebar that indicates the type of family that a gene is actually associated to it. Dataframe 1 BGC1 BGC2 …
bioinformatics_student
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R heatmaply: Show high-expression values on top

Heatmap with high expression values on the bottom I'm quite new to Rstudio and I'm trying to make a heatmap using the heatmaply function in r, but in some heatmaps (with different data) the high expression values (in red) show on top, and with…
Lindsay98m
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How to calculate the cophenetic similarity between two individual in two dendograms or between two clustering methods?

How can I calculate the cophenetic distance for an individual within two trees (not between two whole trees)? I want to calculate the similarity/dissimilarity in position per individual within two dendrograms and show the result in the row color of…
Niels Zondervan
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How to change color of heatmap plot in heatmaply using dropdown menu in R?

I would like to change color of heatmap plot in heatmaply using dropdown menu in R. I wrote below code but doesn't work properly. Thank you for your help in advance. df<- structure(c(5.91907, 3.05747, 5.73896, 5.30454, 4.74619, 6.60657, …
Ati
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troubleshooting heatmaply: how to remove numbers from dendogram

I am integrating the heatmaply package into a shiny app that allows users the option to cluster either by row, column, both, or none. However when the either row or column is selected, the dendogram shows up with numbers as shown in the figure…
Eddy Zavala
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adding row names to heatmap using heatmaply

I am drawing a heat map of some gene expression in Rstudio, but the row names (which should be samples or gene names) are replaced by numbers. I have checked some posts but no chance. sorry if it is a simple question or duplicate, I am new in R.…
Farbod Emami
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heatmaply + flexdashboard = Error in validateCssUnit(sizeInfo$width) : CSS units must be a single-element numeric or character vector

--- title: heatmaply and flexdashboard don't mix... output: flexdashboard::flex_dashboard --- ### Chart 1 ```{r} library(heatmaply) heatmaply(mtcars) I saw this question (2018): R shiny error: Error in html tools::validateCssUnit(height);…
Manor Askenazi
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Heatmaply sidebar colors, how to show specified colors correctly?

I have a problem, might be a bug in heatmaply or plotly. Colors in the sidebar of a heatmap are not showing the colors I specified. See the code example below, At the end of the code in part # 6) the first plot, plotted using the plot function…
Niels Zondervan
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