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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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Drawing a heatmap for 2 columns: Time Vs. Electricity

I have dataframe of 2 columns; where first column holds data as d/m/y h:m (for one year) while second column holds electricity meter reading. For instance: Date.Time X 13/12/2014 12:00 164 13/12/2014 12:30 278 13/12/2014 13:00 …
USAL
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how can I plot one heatmap using two data sets

all existed answers are not working for me! these questions are making the heat maps side by side, to display two heatmaps in same pdf side by side in R or Side-by-side plots with ggplot2 or others I have two dfs which I want to plot the 10 highest…
user1267127
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How can I combine several heatmaps using R in a signal figure

I have created 36 heatmaps with the function pheatmap, and I want to display them in just one figure. I have tried to using the function par(), but it did not work, I do not know why. Could someone tell me what should I do? Thank you very much. This…
Zihu Guo
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Problems with pheatmap usage

I'm trying to play around with pheatmap and getting stuck at the very beginning. Creating a toy example: library(pheatmap) set.seed(1) my.mat <- matrix(rnorm(90), nrow = 30, ncol = 30) rownames(my.mat) <- 1:30 colnames(my.mat) <- 1:30 col.scale =…
user1701545
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map colours to values in heatmap (pheatmap)

A simple question, although I'm not able to figure out how to solve it. I have a dataframe and I've plotted its values using a heatmap by means of pheatmap. The values range in this dataframe is from 0.098 to 2.94. My data has a lof of 1s. I Would…
user2380782
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heatmap like plot with different sets of colors for different data

I'm trying to join different type of data in the same heatmap plot. But I need to use different set of colors for each of the sub-data. Here is an example: data1 = matrix(c(1:9),nrow=3) color1 = colorRampPalette(c('red','blue'))(max(data1)) data2 =…
user31168
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How to Create heatmap in R with post clustering information

I have a data looks like this. Genes Sample cluster 1: ARID1A TCGA-2 cluster 1 2: FAT1 TCGA-2 cluster 1 3: KMT2C TCGA-1 cluster 2 4: KMT2C TCGA-3 cluster 3 5: ATM…
Aryh
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Seeking help to generate a similar heatmap as attached

I am trying to generate a heatmap as the following figure. I have already tried pheatmap and the code is as follows: breaks_2 <- seq(min(0), max(2), by = 0.1) pheatmap::pheatmap( mat = data, cluster_cols = F, cluster_rows = F, scale =…
Raha
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How to force the row labels in a fixed width and be aligned in pheatmap in R?

Usually there is no problem to show the row labels in pheatmap in R. However, see I have a little bit complicated row labels which are strings that combined a head of one string and an end of another string. For example, "ABC**** 123". Here is an…
Sugus
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‘RColourBrewer’ is not available (for R version 3.6.1)

I'm trying to create a heatmap using gplots, but can't install RColourBrewer. I think I'm using the latest version of R. Do I have to uninstall it and reinstall an older version of R that is compatible with…
Shiranui42
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change levels of column names of a matrix for plotting heatmap

I have my matrix and I'm ready to plot a heatmap using the pheatmap package in R. My matrix is like: Name A B C Apple 1 2 3 Banana 4 5 6 Pear 7 8 9 If I don't cluster the column, the heatmap will order the columns as A, B and C. What if I want to…
Lennon Lee
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RNS seq analysis, using R, make pheatmap, all looks blue

1[enter image description here]2 I am trying to make heatmap using pheatmap fucntion. My problem is always all the values between high and low are showing as same color. Is there any way to show more dynamic heatmap picture?
Sun Kim
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Re-Classifying data

I have made matrix using pheatmap and need to be able to reclassify it into 8 classifications. Any help would be greatly appreciated and I have placed the code below. pheatmap(y, cluster_row=FALSE, cluster_col=FALSE, display_numbers=TRUE, …
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