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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 change the color of values that fall outside the determined breaks of the pheatmap function in R

I have 1 question regarding the pheatmap function in R and would be extremely thanksful if anyone could help me out. 1) When doing pheatmaps, I always set my breaks using the break function. However, if a value fall out of the determined breaks it…
gabo
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pheatmap: Error in col[as.numeric(cut(x, breaks = breaks, include.lowest = T))] : object of type 'closure' is not subsettable

I am trying to generate a heatmap with the pheatmap package, however, I keep coming up against various issues (I am new to R). The code I am using is: pheatmap( mat = newdata, color = colorRampPalette, border_color …
Leeanne McCarthy
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Change color of one annotation in heatmap R

I am doing a heatmap in R. I have several annotations in the Exam$Design and I would like to change the colors of the annotation 'condition' because as you can see from the plot they look very similar but in fact are not (as seen in the legent there…
Carlotta Porcelli
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R: how to set p for minkowski distance in pheatmap?

In R, there is a function to generate heatmap with dendrogram, called pheatmap::pheatmap. minkowski is one of the distance measuring options for pheatmap to draw dendrogram. However, how to set the p (The power of the Minkowski distance) in function…
WCMC
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How to select which is the best cluster or top cluster for rows when using kmeans_k in pheatmap?

In an earlier post of mine I did kmeans_k clustering in an iterative process in pheatmap package to reduce my rows(genes) from 90 to a stricter subset. This I did since when I tried to test optimal clusters on the rows with packages the factoextra,…
ivivek_ngs
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Set color range in pheatmap

I am new to R and started using pheatmap to visualize log2 fold changes in gene expression in treated vs control cells. By default, pheatmap sets the upper limit of the color key to 6 and the lower limit to -2. Is there a way to assign the colors in…
DP_LMU
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extracting members of cluster (pheatmap)

I am performing cluster analysis and using pheatmap function in R. I want to extract each member of the cluster. The command that I am using to generate pheatmap with kmeans clustering is: pheatmap(t, kmeans_k=65, cluster_cols=F,…
Angelo
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Which color-key to use in a heat-map with a small range of values?

My data covers a small range, but I still like to make the small differences between the data points visible in a heat-map. What color-key is best to maximize color intensity (and not generating a greyish map) and how to set the range in pheatmap?
Joanne
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Plot grouped values of a dataframe in R

I have the following dataframe: stat mTADs DE_genes 5267 -5.452819 chr2:167337500-167447500 chr2:167318145-167341673:+ 5268 4.114012 chr6:41532500-41642500 chr6:41555481-41570508:+ …
user2931662
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How to disable the continual color annotation in heatmap

library(NMF) # other packages are welcome car<-as.matrix(cars) car[car<18]<-0 car[car>=18]<-1 aheatmap(car) I would like to see only two colors in the legend: the 0 represents blue and 1 represents red.
Ming
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how to reverse the color of row legend in heatmap?

I would like to reverse the default annotation for row: library(NMF) #any other packages for this task are welcome car<-cars car$p<-sample(1:600, 50)*0.0001 aheatmap(as.matrix(cars[,1:2,drop=FALSE]),annRow =car[,"p",drop=FALSE]) As you can see…
Ming
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Clustering strategy given a known treatment

Is there a strategy to cluster shared attributes within a group across a condition, knowing that the condition should inspire a difference between two groups? A concrete example: say there are 4 individuals in Group A and likewise 4 in Group B.…
batlike
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Is it possible to make a heatmap with 200k rows?

I would like to know if it is possible to make a heatmap with 200k rows? I have a matrix with genomic coordinates as rows and each column represents the presence or absence of that region in each patients. so I have 15 patient (columns). Now when I…
ivivek_ngs
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Can you extract the data matrix from pheatmap in R?

I created a heat map based off of gene microarray data and then used the pheatmap to cluster the data and output a heatmap. Is there any way to output the clustered data of the heatmap in a matrix form to an excel file?
K. F.
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Cluster annotations using pheatmap

So, I am trying to create a pretty heatmap with pheatmap function in R. I want to have coloured bars where the dendrogram stops and the graph starts in order to annotate the different clusters. Like a horizontal thick line running through columns…
Kwnwps
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