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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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how to increase labels distance from main plot in heatmaply r

I have a simple issue in interactive heatmap in R. I couldn't figure out how to increase margins (distance between x and y labels with main plot) in heatmaply? I want to add a little bit of space in ylab (province) from heatmap. Could anybody help…
rez
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Is there a way to specify number of kmeans clusters to return in heatmaply

I would like to return a specific number of clusters for my interactive heatmap from heatmaply like I can do with pheatmap and the kmeans_k = argument. Is there a way to do this with heatmaply? If I have a large matrix and do not define the number…
jLuthy
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R: Heatmaply creates empty/ white space in viewer

i tried to create a heatmap with my own data and kept only getting white space. I found this very basic instruction on how to work heatmaply based on the mtcars data. After restarting R (close Window and reopen, not build-in restart) I tried and…
BeccaLi
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Using heatmaply dendrogram sorting in pheatmap

Is there a way of using the dendrogram clustering method used in the heatmaply package and to apply it to a heatmap produced by the pheatmap package? Basically the opposite to what was asked here: Clustering in pheatmap and heatmaply R packages I…
jpquast
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R heatmaply and pheatmap output

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 color output I get using the pheatmap package. Therefore, I would like the two commands to produce the same…
Arturo
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Use heatmaply to create heatmap with raw values/data without transformations?

When creating a heatmap with heatmaply::heatmaply(), some transforms are performed on the raw data. This is evident in the following example where some of the iris dataset is provided, yet hovering over the heatmap shows some negative values (which…
dss
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heatmaply: adjust the colour

I am using the package heatmaply to visualise single cell expression data. I want to use custom colours and to assign "yellow" to expression levels > 2 , "magenta" to expression levels < -2. The range between [-2,2] should be represented by smooth…
tanya subkhankulova
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Get the name and values of second member of cluster made at stage1(contains two members only) of heatmaply given the name of one of the members

I have a data frame S=[rows x cols] containing samples s such that rownames tell the names of the samples and colnames tell the features of the respective samples. In this data frame, i have inserted one test sample t1. Now i want to extract the…
Aslan
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How to assign correctly low, mid and high color limits with heatmply R package for an interactive heatmap

based on a current visualization project for ngs experiments and functional enrichment analysis results, I'm trying create an interactive heatmap plot of specific biological processes-names in the rows, and specific annotated genes in the columns,…
Jason
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Issue with heatmaply when using navbar in shiny

EDIT: I have simplified the application and make it all the code reproducible. EDIT 2: I just discovered that when I use the navBarPage I must click on Additional Parameters -> Colour. Then is coloured as expected. I'm developing a shiny app which…
Nadrieci
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How to have an additional coloumn in a heatmaply heatmap

I am using heatmaply to obtain clustered heatmaps of responses from multiple raters on a series of questions rated using the same Leikert scale (ECOG Performance Status). The heatmap comes out well (though using hierarchical clustering on ordinal…
Santam
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selection the classes of observations using heatmaply in R

The simple example library(heatmaply) heatmaply(mtcars, k_col = 2, k_row = 3) %>% layout(margin = list(l = 130, b = 40)) and we get this plot We see that the observations were divided on 3 clusters 1 from honda civic to ferrari dino 2 from valiant…
psysky
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Error in heatmaply package in R

I would like to create an interactive heatmap plot for my dataset (3109 rows and 12 columns) using heatmaply package in R but got below error: If I remove the rownames I wouldn't get the error but I need to see the names at least in each spot in the…
Ati
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How to fill with grey50 in cells where value=NA and show values in cells where value!=NA in a Heatmap using heatmaply?

I would like to fill with grey50 in cells where value=NA and show the values in dark2 in cells where value!=NA as in the heatmap from Palpacuer et al. Could anyone help me, please? Here are my data and code: T<-c("Pla", "Ond","Gra", "Dol","Tro",…
Krantz
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correlation heatmap using heatmaply R

I'm trying to create an heatmap on the base of spearman correlation and with dendrogramm corresponding to spearman correlation values. My input file is composed as follow: > data[1:6,1:6] group EG PN C0 C10 C10.1 1…
Dr.PhilCol
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