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Questions tagged [pheatmap]

A package for drawing pretty heatmaps in R.

pheatmap is a package for drawing pretty heatmaps in R. The ordinary heatmap function in R has several drawbacks when it comes to producing publication quality heatmaps. It is hard to produce pictures with consistent text, cell and overall sizes and shapes. The function pheatmap() tries to alleviate the problems by offering more fine grained control over heatmap dimensions and appearance.

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How to draw pheatmap plot to screen and also save to file

I'm working with the pheatmap package. By default, it draws the plot to the screen. In my case, that means output in a R markdown notebook in R studio. But I also want to save to a file. If I save it to a file, giving it the filename= argument, it…
Alex
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R pheatmap: Perform clustering and show dendrograms PER ANNOTATION CATEGORY

I know how to group rows (genes) by annotation category using pheatmap, and I know how to perform Person's correlation clustering on the whole set of rows (genes), but what I would like to accomplish would be to perform clustering (and show…
DaniCee
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Google heatmap not showing data points properly

I am facing a strange problem with google heatmap. Heatmap shows less datapoints on increasing number of coordinates in heatmap data. For 333 coordinates, heatmap shows datapoints like: And for 9885 coordinates : As you can see for 333 coordinates…
user1234
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Edit row and col names in Pheatmap

I want to edit row and col names in my pheatmap or eventually delete and add new row and col names to be edited. In this case I will set show_colnames and show_rownames to FALSE. library("pheatmap") pheatmap(scale(dat), show_colnames = T,…
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pheatmap scale="row" giving Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call

I am trying to create a heatmap with gene expression values with the package pheatmap in R. I have used the code numerous times and never had a problem untill today. It seems when I do the scale="row" , I end up with this error. I cannot create the…
ivivek_ngs
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Pheatmap:Error in annotation_colors[[colnames(annotation)[i]]] : subscript out of bounds

library(pheatmap) another<-read.table("~/Desktop/tcga3dcategorized.csv",sep=',',header=FALSE) test<-another[1:3] labels<-another[4] colnames(test)=c("Dim 1","Dim 2","Dim…
Greenhand001
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Pheatmap display_numbers argument

I need to use and show stars for significances within my pheatmp, I have utilised the approach below. As you can see the stars reported by the figure cross the cell border. Is there a way to centre it within the cell? test_vals <- matrix(rnorm(20),…
Al14
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Error in check.length("fill") : 'gpar' element 'fill' must not be length 0

I faced a very weird error, possibly a bug in R 3.5.1 or pheatmap The following code is working fine: rownames(df) <- colnames(mat) xx <- pheatmap(mat, annotation_col=df) But the following is not working: rownames(df) <- str_sub(colnames(mat), 1,…
Nikita Vlasenko
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Clustering within groups with pheatmap

I am trying to make a heatmap showing gene expression across 4 different groups, and I would like to cluster within each group. I have samples sorted by group across the columns. Using cluster_cols = True clusters across all groups, mixing up the…
gtresto
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R: pheatmap reorder columns while maintaining topology

I would like to change the column order of my heat map created with the R package pheatmap, but keep the same topology so that the dendrogram on top also reorders with the columns. While explained in the documentation, I can't figure out how to…
Sam Vanbergen
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pheatmap default distance metric R

I need to make a heatmap with the function 'pheatmap', using UPGMA and 1-pearson correlation as distance metric. My professor claims this is the default distance metric, although in my case it uses 'Euclidian' as distance metric. Is euclidian and 1…
Sam Vanbergen
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How can I increase the margins for the R function, pheatmap?

I am plotting a heatmap using pheatmap (Documentation). I am plotting a matrix in a fairly straightforward way: pheatmap(mat, annotation_col=df, labels_col=rld$Infection_Line, fontsize_row=5, fontsize_col=7) The bottom of my plot is getting cut…
Adam Price
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Multiple panel plots with pheatmap

I am trying to do multipanel plots one panel being a heatmap using layout to place plots. I've been drawing heatmaps with pheatmap which provides a very convenient color scheme among other things. The code for pheatmap is available here. When I try…
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pheatmap in R. How to get clusters

I'm using pheatmap with large data. My purpose is to clusterize rows and columns and to analyze main clusters. I upload the data table and perform the heatmap as follows: library (pheatmap) data<-read.table ("example.txt", header = TRUE) …
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pheatmap formatting in R: Legend size and creating a square plot

Pheatmap only creates a square plot when legend=FALSE. I have tried using par() to allow more oma() and mar() space without luck. The legend is also really big and i cannot find any documentation on reducing this or changing its position. The first…
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