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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 sometimes not rendering in Shiny

I have a complex Shiny app with hundreds of reactive elements. The problem is that sometimes pheatmap plots don't render, and I have to restart the app to make it work. This has been the case with all different pheatmap plots with no shared data or…
Rasmus
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Making a continuous color chart for heatmap using pheatmap

I'm looking to figure out how to use the pheatmap package and to make a continuous color coded heatmap. I would like to use three colors, red, white and blue to for my map, where white = 0, blue is for negative numbers, and red for positive. I want…
SpiderK
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Zooming in on pheatmap in Rstudio

I generated a heatmap of some single cell data (3285 cells x 6000 genes) using the pheatmap package on Rstudio. The columns are different individual cells, and the rows are different genes. I was able to find a pattern looking at the heatmap, and…
user18219937
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Adding metadata as annotation to correlation heat-map

I m trying to generate a sample to sample correlation heat-map which I m able to do it. Is it possible to add metadata to the correlation heat map just as we can do for normal heatmap? My code library(Hmisc) library(pheatmap) df1 <-…
PesKchan
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R: Convert a string to list object name for pheatmap annotation colors

I am trying to automate code for making pheatmap color annotations. So that I do not have to personally annotate each sub sample. However, I can't figure out how to convert the string from a factor/ object name. Is this possible? I just receive an…
Ed_
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How to put legends at the bottom of the heatmap,still not solved?

[ Reference: ] [3 differences : Question1:how to make the legend on…
user17234955
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Heatmap of Gene intensity values in R

I have data that look like…
Huzaifa Arshad
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Assigning specific color to a range of values in heatmap using pheamap

I want to make a heatmap using pheatmap where if anything is between -1 to -0.5 it should be darkgreen and anything between -0.5 to -0.10 as lightgreen and anything between -0.10 to 0 as white. Similarly 0 to 0.10 as white, 0.10 to 0.5 as light…
user3138373
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pheatmap: color each row of a matrix independently using a gradient from max to min

I am trying to show the colors for each row in my matrix (min to max gradient): [1,] 8 12 11 5 24 [2,] 1 2 7 0 8 [3,] 53 99 1501 15 9859 [4,] 59 24 19 19 32 [5,] 4 2 11 0 68 [6,] 4 9 177 2 710 [7,] 2 1 2 2…
Process1
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Keeping the pheatmap color range the same for different heat maps

I have the following code to make two different pheatmaps representing correlation matrices. A1 <- c(1,2,3,4) B1 <- c(2,4,3,1) C1 <- c(2,4,3,5) D1 <- c(2,3,1,4) E1 <- c(2,1,4,5) Gene <- c(1,2,3,4) df1 <- data.frame(Gene, A1, B1, C1, D1,…
Dswede43
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difference between corrplot and pheatmap of correlation matrix? how to make it consistent between the two

I noticed that the correlation plot made by corrplot is different from the one made by pheatmap. original data: enter link description here correlation matrix in corrplot, count = read.csv('data_here.csv') mtx = cor(count, method =…
Hh Xu
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Error in RColorBrewer::brewer.pal(n, pal) : NA is not a valid palette name for brewer.pal

I am trying to annotate data points in pheatmap. Everything works fine up until plotting the heatmap. data <- as.matrix(Round_1) library(pheatmap) …
A Z
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unable to make scaled heatmap for diffrential gene analysis

Im new to R so be easy on me, I'm having trouble generating a heatmap for my genes. I performed diffrential gene analysis using DESeq2 package and found the 30 most downregulated genes and with fdr<0.05 for cell lines. I was trying to create a…
Halake
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pheatmap: not printing over text when changing color of text on axis

Is there a way to get pheatmap (in R) to not write over the row_names with new, colored text, if I change the color of the text? By default, the color of the row or column text is black, but with a little tweaking, one can change the color of the…
Purrsia
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Can I show only a part of my heatmap e.g. the upper part?

I have a big dataset with around 1000 significant hits calculated by anova. I can draw a beautiful heatmap using the pheatmap package. However, the heatmap is huge and I would like to look at bigger clusters in more detail. Can I somehow hide parts…
doodles
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