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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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can i change the column names to the top in PHEATMAP

I am using PHEATMAP to generate a heatmap - currently the row names and column names defaults to left and bottom - can somebody point me to option where i can change it to RIGHT and TOP.
Neo
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HEATMAP/GGPLOT R

I am trying to create competency level heatmap for a manufacturing plant.I have tried both the HEATMAP as well as GGPLOT. I have couple of questions when it comes to using GGPLOT- here is the sample data. I am still not sure which will yield me the…
Neo
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Increasing left length branch in dendrogram (pheatmap)

I found this topic and I would like to got similar result plot. I am trying to plot a heatmap with the library pheatmap in R and I need to increase the left branch size. I would like to decrease the colored area and increase dendrogram branches. I…
Tatui1969
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Pheatmap won’t cluster rows: NA/NaN/Inf in foreign function call (arg 10)

I have been using the same variations of a pheatmap code to make heat maps for several months now without any problems, but lately it has stopped being able to cluster rows. Columns still cluster like normal but whenever I try to add row clustering…
paige
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Glitch in pheatmap() condition grouping, along with other points of confusion

I wanted to have my conditions labelled on the heatmap I am making for DGE. This code: mat <- assay(rld)[topVarGenes,] condition = c("black", "orange") names(condition) = c("Dark", "Light") ann_colors = list(condition = condition) pheatmap(mat,…
rachelbasch
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How to plot heatmap with R shiny

I am working with R shiny for pheatmap, I want to read files and draw heatmaps, but it did not work. The csv file could be read, however, the content could not be seen from the web, and the heatmap could not be…
Runbin Sun
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missing annotations and colors in pheatmap

Using pheatmap R package, I need to make a heatmap with annotations of a custom color set. I use the following code: ### Make a matrix mat<-replicate(23, rnorm(23))…
Grant
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Heatmap for a relationship matrix with user-defined colorbar

I would like to draw a heatmap of an interrelationship matrix to show the distance from 1. I have made a heatmap as below, but I would like to have the colour defined according to the distance from 1; the further the number, the lighter the color…
Lisa
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pheatmap: change text color

How can I change the text color in pheatmap? I've tried the following but it doesn't change the axes text and labels but it doesn't work par( col.lab="#FFFFFF", fg="#FFFFFF", col.main="#FFFFFF", col.axis="#FFFFFF", cex.main=2,…
vmontazeri
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Heatmap with multiple/stacked variables per individual

I am trying to create a heatmap. Each individual has three binary variables (ecz, whz, rhi) across 6 time points. The attached heatmap isn't at all informative as I want to see how the variables develop concurrently. For each individual rows), I…
SK77
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R pheatmap: use logarithmic scaling in the legend

I have a matrix library(pheatmap) set.seed(1) mat <- matrix(rexp(200, rate=.001), ncol=20) pheatmap(mat) and there is one value that is much higher than the rest. Therefore, I would like to use a logarithmic scaling for the legend bar (1, 10, 100,…
Revan
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change line width of dendrogram in pheatmap in R

I have used single cell RNA-seq data stored in a single cell experiment assay to perform hierarchical clustering of ~ 11.3000 expressed genes (not clustering samples) using pheatmap in R to show the heterogeneity of the data. I need the output image…
RBorup
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RMarkdown: Creating two side-by-side heatmaps with full figure borders using the pheatmap package

I am writing my first report in RMarkdown and struggling with specific figure alignments. I have some data that I am manipulating into a format friendly for the package pheatmap such that it produces heatmap HTML output. The code that produces one…
C. John
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Heatmap with customized color scale bar for values below and above thresholds

I would like to make an heatmap in R using pheatmap with the colors green, black and red and using a range in the legend from -2 to 2, here is the code that I used: library(pheatmap) my_palette <- colorRampPalette(c("green", "black", "red"))(n =…
user40267
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is there a way to preserve the clustering in a heatmap but reduce the number of observations?

I have data-set with 90 observations(rows) across 20 columns. I have generated a pretty neat heatmap which clusters my data in two groups with the package pheatmap. Although its not entirely clean but the two clusters of dendrogram pretty much…
ivivek_ngs
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