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Pheatmap

Manufactured by Posit

Pheatmap is a powerful tool for visualizing data in the form of a heatmap. It allows users to create highly customizable and informative heatmaps, which are a widely used technique for exploring and presenting patterns in multivariate data.

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2 protocols using pheatmap

1

Differential Gene Expression Analysis

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Differentially expressed genes of four tissues were filtered by the same criteria, which were 1.5-fold expression difference and p-value < 0.05. Volcano plot and heatmap were constructed by ggplot2 (v3.3.5, RStudio) and pheatmap (v1.0.12, RStudio), separately. Venn diagram was plotted by VennDiagram (v1.7.0, RStudio). Differentially expressed genes were further analyzed by Gene Ontology (GO) in terms of molecular function, cellular component, and biological process.
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2

Statistical Analysis of Biological Data

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Statistical analysis was performed using Prism 7 (Graphpad, La Jolla, CA) or RStudio (RStudio Team, 2015 ). For comparison between two groups, an unpaired T-test was used. For comparison between multiple groups, a one-way ANOVA was used with multiple comparisons to the control. Distributions were compared using a chi-squared test. Correlations were assessed using Pearson correlation co-efficient with two-tails. Graphing of the data was performed using Prism 7. Additional visualizations were created using ggplot2 (Wickham, 2009 ) and Pheatmap (Kolde, 2012 ) package for RStudio (RStudio Team, 2015 ). Vector diagrams were modified using Graphic (Autodesk). Statistics for differential gene expression from transcriptomic studies were performed at a dataset level with a False Discovery Rate (FDR) of 0.05 and represented in the graphs as such. An α level of 0.05 was used for all analyses. All values are means ± SEM unless noted otherwise. Asterisk (*), (**), (***) and (****) indicate experimental pairs where differences between the compared values were statistically significant (P < 0.05, P < 0.01, p < 0.001 and p < 0.0001, respectively).
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