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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.

58 questions
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Plotting a clustered heatmap with dendrograms using R's plotly

I'm following this example on how to create a clustered heatmap with dendrograms with R's plotly. Here's the example: library(ggplot2) library(ggdendro) library(plotly) #dendogram data x <- as.matrix(scale(mtcars)) dd.col <-…
user1701545
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Dendrogram with Corrplot (R)

Does anyone have a method to adorn an R corrplot correlation plot with a dendrogram?
abalter
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Heatmap in R with raw values

I have this dataframe: df <- data.frame(PatientID = c("3454","345","5","348","567","79"), clas1 = c(1, 0, 5, NA, NA, 4), clas2 = c(4, 1, 0, 3, 1, 0), clas3 = c(1, NA, 0, 5, 5, 5), stringsAsFactors =…
Lili
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heatmaply color when all elements are the same value

I'm using heatmaply to generate "heatmaps" of binary matrices, where each value in the matrix is a 1 or a 0. I've set 1 to red and 0 to gray, and it works fine. The code looks like so: library(tidyverse) library(heatmaply) dummy_data <-…
Ram RS
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How can I deploy an interactive heatmap by shinyheatmaply

I am trying to deploy an interactive heatmap as a shiny app but not simply an interactive heatmap rather a fancy heatmap by shinyheatmaply but when I am running deployapp nothing happens This is my…
fi1d18
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heatmaply Can't Reorder without Displaying Dendrogram

I wish to reorder the rows but not show the dendrogram with heatmaply, this code runs but doesn't do this: colorStand <- colorRampPalette(colors = c("blue", "white", "red")) heatmaply(data, margins = c(60,100,40,20),colors=colorStand,limits =…
RJVV
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Interactive heatmap in R

My dataframe looks like: rankA rankB V1 V2 1 0-1 w 1-2 t 8.636042 10.43002 2 0-1 w 3-5 t 6.495266 10.52126 3 0-1 w 6-10 t 5.480639 10.56230 4 0-1 w +10 t 4.897840 10.64759 5 …
Mario M.
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Is there any option to export the heatmap from heatmaply in .svg format

I am wonder if there is any option to export the heatmap in svg or pdf format.
Carlos Henríquez
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How can I plot a heatmap with the heatmaply package in Shiny?

I am trying to use the heatmaply package in order to plot a heatmap and it works well. On the other hand, when I try to do the same plot in Shiny it doesn't appear in the interface (when I click "run app"). However, when I close the window suddenly…
emr2
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Identify cluster number in dendrogram from heatmaply

I am using the heatmaply package to create heatmaps with dendrograms from the dendextend package. Is there a way to identify the cluster numbers on the dendrogram? This is an example heatmap for the mtcars dataset. I want cluster numbers on the…
Sara Altamirano
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How to add an interactive heatmap to a PDF?

I have created a heatmap in R and heatmaply. I need to add this heatmap to a paper I am publishing. The heatmap is very big and heatmaply's zoom is very useful. Is it possible to add this heatmap - it becomes a .html file when saved - to a PDF? Is…
Omkar Sabnis
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Get row names belonging to each cluster from heatmaply clusters in R

I am trying to get 5 lists of all row elements after using heatmaply in R. I set k_row = 5 so the dendrogram shows 5 different colors. I just want to return a list of 5 lists, where each list contains the row elements within a cluster. The rows are…
amc
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Remove row labels from aheatmap and heatmaply (heatmapr)

I would like to remove the row labels from a heatmap with many rows. I need to do this in both heatmaply and aheatmap. However, all the possible options I could think of either result in an error or relabel the rows from 1:nrow and show the numbers…
datapointier
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Overlapping labels in heatmap

I am making an heatmap with "heatmaply" R package, but I have overlapping rownames (see red circled area). Any suggestion or tutorial about fixing this problem? Thanks a lot!
Edoardo Scali
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excluding heatmaply row_side_colors

I'm trying to make a basic heatmap in RStudio using heatmaply. My data look like this: I tried these commands: eg <- read.delim(file="example_heatmap.txt", header=T, sep="\t") heatmaply( file="heatmap_eg.png", height=2000, eg, …
Mir Alvee Ahmed
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