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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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Pheatmap Color for Specific Value

I am very new to R and recently I have been playing around with the pheatmap library to generate, well, heatmaps. My problem is that I want to color my heatmap in a specific way. I'll describe below: Values < 1 should be a color ramp (e.g. dark…
Dave
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How to take a sample from a large plot to show in knitr-PDF

I often create large plots in RStudio which I save to PDF but would also like to partly show in the PDF knitr report. Is there a way to create the full object then cut a piece (ideally top left corner) and include that second picture in the PDF…
splaisan
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R - Extract (p)heatmap colors to use in polygon fill

I created a heatmap in R which is n*k in size, is it possible to extract the individual colors used for an ith element? For example n=3 (columns) and k=50 (rows), n is an arbitrary level of severity and k represents a district in the UK. I have…
Al OLoughlin
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how to create discrete legend in pheatmap

I want to create a discrete legend (not continuous) in pheatmap. So for this code, m=as.matrix(c(1:100)) breaks=c(1,5,10,50,80,100) color=c("red","blue","green","yellow","orange") pheatmap(m,cluster_rows=FALSE,…
pcantalupo
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How to merge heatmap with goplot in R ggplot?

I created a heatmap using pheatmap package as follows: test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3 test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2 test[15:20, seq(2, 10, 2)] = test[15:20,…
user2110417
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R pheatmap How to plot a linear model?

I have a classical linear model y ~ x1 + x2. How can I plot a heatmap of this model? Normally I print a heatmap from data in this way: library(pheatmap) data <- data.frame(y=c(1,2,3), x1=c(1.5,2,2.5), x2=c(3,10,12)) pheatmap(cor(data),…
user3351676
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pheatmap: manually re-order leaves in dendogram

I have created a heatmap with a corresponding dendogram based on hierarchical clustering with {pheatmap}. I would like to change the order of the leaves in the dendogram, manually, based on what I see visually. First, can anyone confirm that this is…
B_slash_
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pheatmap with larger gap_col in R

In R function pheatmap::pheatmap, is it possible to adjust the gap distances? In the following example, I created a gap in columns 3 and 4 using parameter gaps_col=3. Yet, the gap is too small visually. I wonder if there is a way to adjust the gap…
Tan
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Pheatmap Annotation Row

Excuse Essay So I’ve done a Deseq analysis, then taken the counts file, applied the same names and then removed an NA values , then created a ?tibble/table called sigs, which I then turn into a Data frame: sigs <- na.omit(res) sigs Looks something…
Rob Staruch
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How to change font family of a heatmap created by the pheatmap package

I would like to change the font family of the following graph to Times New Roman, but couldn't figure out how. Any help will be greatly appreciated! A reproducible example: d <- data.frame ( c(runif(5, min=0, max = 5)), c(runif(5, min=0, max =…
stephany
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R pheatmap: How to color specific row names while omitting column names?

Using the "pheatmap" package in R, with Rstudio for Windows 10, I can follow an example(as shown here) to produce a heatmap with selective coloring of row names as long as the heatmap displays both row and column names. However, if I try to generate…
Hypersphere
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plot heatmap in R in linux

I am trying to plot heatmap in linux. this is the script i have written: #!/bin/R setwd("~/scratch/peerfactors") library(readr) library(png) #install.packages("Pheatmap") library(pheatmap) r_80 <- read_table2("GVDS_predixcan_n80.txt") d <-…
Rhea Bedi
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Changing the colour palette based on quantile values in pheatmap

enter image description hereI am very new to R and I am trying to make a pheatmap out of my data. I just copied some existing code included in a tutorial and it seems it pretty nicely fitted to my data after some tweaking. I also included some…
Lukáš Konečný
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Automatically categorize and add annotations using pheatmap in R

I have a dataframe made by the school grades of some students in different subjects. The students are also characterized by their gender (F or M), that is included as a suffix in their names (e.g. Anne_F, Albert_M, etc...) With these data I have…
EmaK
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Clustering differences between pheatmap and corrplot() using ward.D2 method

I have performed Spearman correlation for my data. Then I tried to cluster and plot my data using the "ward.D2" method for corrplot()and pheatmap(). However, the order of the variables is different between the two plots. Could someone help me…
Geli
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