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PHeatmaps specifications


Unique identifier OMICS_26726
Name PHeatmaps
Alternative names Pretty Heatmaps, pheatmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.9
Stability Stable
Maintained Yes




No version available



  • person_outline Raivo Kolde

Additional information

PHeatmaps citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] mples was carried out with DESeq2. For the visualization of gene expression and unsupervised hierarchical clustering of the samples the rlog normalization in DESeq2 was applied. We used the R library pheatmap for sample clustering (euclidian distance, complete linkage clustering) and heatmap.2 from the gplots package to visualize differentially expressed genes (Pearson correlation and ward.D clust […]


FACS Seq analysis of Pax3 derived cells identifies non myogenic lineages in the embryonic forelimb

Sci Rep
PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1
call_split See protocol

[…] ff of p ≤ 0.05, with a fold change ≥1.5, between any two consecutive time points. Principal component analysis was performed using the prcomp function in R software. Heatmaps were generated using the pheatmap package in R software. Signed difference ratios (SDR) were calculated similar to, except the average for each gene across all samples was subtracted from each sample. Fastq sequences were dep […]


Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] Significant correlations were defined as a correlation coefficient (r) of over 0.05 (or less than −0.05), with a pseudo-P value of ≤0.05 (). Heatmaps of the correlation were generated in R using the pheatmap package. We performed hierarchical clustering for both columns and rows with the average linkage method using Pearson’s correlation. We utilized PICRUSt v1.0.0 to construct a predicted metage […]


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] 3). A list of 72 genes of interest was used for clustering by multidimensional scaling using the base R package stats. Spearman correlation based on those 72 genes of interest was performed using the pheatmap package. FPKM values for each cell were median-normalized and used for Spearman correlation based on the expression of the same set of genes of interest. For the tenfold enrichment analysis, […]


Genome wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon

BMC Genomics
PMCID: 5954288
PMID: 29764387
DOI: 10.1186/s12864-018-4457-8

[…] lected to perform hierarchical clustering. The normalized RPTM values plus one were log scaled to calculate correlation coefficient (CC) values between samples. Then the CC values were applied to the pheatmap function in the pheatmap library in R to perform hierarchical clustering. miRNAs with average abundances of at least 5 RPTM in the 14 samples were used to perform Principle Component Analysis […]


Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes

PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] scatter plots were generated using scatterplot3d_0.3–40 package, and bar plots, dot plots and two-dimensional scatter plots were generated using ggplot2_2.2.1 package. Heat maps were generated using pheatmap_1.0.8 package. […]


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