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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 make hierarchical cluster pheatmap in r?

I have use this code to make hierarchical cluster heatmap but no color is coming library(tidyverse) Mydata <- structure(list(Location = c("Karnaphuli River", "Sangu River", "Kutubdia Channel", "Moheshkhali Channel", "Bakkhali River", "Naf River",…
Kazi
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Remove NAs from non-selected rownames in pheatmap in R

I have a selected group of genes I would like to plot which I have renamed. But when plotting them I also get the NAs for the non-selected. How could I remove the NAs only plotting my selected genes? library(pheatmap) set.seed(2020) mat =…
Ecg
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Color scaling in pheatmap

I've made this heatmap of a correlation matrix for a class. I want to fix the color scaling, specifically for infection_status. The pink shades its chosen are to similar not just to infections tatus but they even look the same as…
Angus Campbell
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pheatmap discrete colormap placement of tick labels

I have a matrix with thousands of cells, with values range from 0-5. I want to use a discrete color palette to indicate the value of the respective cell. This code already works pretty well, but the position of the colormap labels is off. I simply…
nhaus
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How to fix heatmap legend out of margin?

I want to increase the font size of the heatmap, but I found when the lengend name is long and legend group name is short, the legend will easily out of margin. Here is the example: test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] =…
Leon Smith
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highlight specific gene name in pheatmap

I would like to ask if there is a possibility to highlight some gene names(row names) in the heatmap package? I want to highlight the row names "I", "H", and "G" in a different color(red color) keep the rest as it is. Here is my…
adR
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Plotting heatmap with R and clustering

hello everyone I am trying to plot the heat map wanted cluster the plot and plot is not looking good wanted change the color i am newbie can any one tell me how can I plot heat-map with clustering values which are showing similar pattern cluster…
Shrilaxmi M S
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Add color with a legend on row from pheatmap

I create a heatmap, I would like to add color on the row with a legend I got this : I would like this a legend with color from only row data : My code is : library(pheatmap) test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10,…
Julie Hardy
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Is there an R function to plot a single variable as a heatmap?

I've generated some RNA-seq data and have my list of DE genes between two groups and fold-changes (log2FC). I'd like to be able to plot a summary heatmap of log2FC for this group comparison in a single bar similar to one in this figure . Would…
guray00
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Improving my Heatmap in R with pheatmap()

Hey I am a complete beginner to R and need to reproduce this heatmap as best as possible in the next couple of days. My data is an xlsx file with multiple sheets, I cleaned it as good as I could and it should be in an okay format. I Have 2…
doc elfein
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Unexpected clusterings using same distance (pearson)

I'm playing with some dummy data to test clustering based in correlation distance (pearson). I'm calculating pearson correlation two ways, one inside the pheatmap function and other outside using cor(), both ways I would expect to retrieve same…
HeyHoLetsGo
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Clustering in pheatmap and heatmaply R packages

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 clustering (ordering of rows and columns) I get using the pheatmap package. Therefore, I would like the two commands to…
Arturo
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pheatmap annotation_colors not using specified palette

I've made a heatmap including colors for annotating the rows using the script from here. Currently my script is this: cols <- colorRampPalette(brewer.pal(9, "Paired")) mycolors <-…
sian
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R: add some text to plotting area in pheatmap

I just want to add a chunk of text inside the plotting area of a pheatmap. Since the pheatmap function already wraps everything within it, I am having difficulty figuring this out. In the MWE below, I just want to add long_text below the plot or,…
DaniCee
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How to extract the heatmap of from a set of gene interest from main heatmap?

I have made a heatmap based on following script. #load the library library(pheatmap) #set label font par(cex.lab=1.5) # is for y-axis par(cex.axis=1.5) # is for x-axis #Set the working…
user2110417
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