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RStudio pheatmap function
Pheatmap Function, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pheatmap+function+in/pheatmap+function/pm40311731-99-22-25
Average 90 stars, based on 1 article reviews

pheatmap function - by Bioz Stars, 2026-10

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Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids
Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio.

Article Title: Variation in protein and amino acids in global collection of pearl millet (Pennisetum glaucum) germplasm
Article Snippet: Means were used to perform Hierarchical analyses based on Euclidean distance based clustering for both traits and genotypes using ‘pheatmap’ function in Rstudio (Posit Team, 2023).

Article Title: Enzymatic hydrolysis method for development of low glycemic index rice flour from temperate grown rice (var. Jehlum): Numerical optimization, rheological and spectroscopic characteristics.
Article Snippet: This study aimed at optimizing process protocols for development of low glycemic index (GI) rice flour (LGIRF) by employing enzymatic hydrolysis method using central composite rotatable design (CCRD).. LGIRF was evaluated for pasting, farinographic, spectroscopic and microbiological attributes.. Independent variables for optimization included concentrations of α-amylase (0.02–0.12 %), glucoamylase (0.02–0.24 %), as well as the incubation temperature (55–80C).

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Article Title: A Guide to Basic RNA Sequencing Data Processing and Transcriptomic Analysis
Article Snippet: .. This heatmap is generated using the pheatmap function in RStudio [9]. install.packages("pheatmap") # the pheatmap function is installed. library(pheatmap) # pheatmap function is loaded. ..

Article Title: Oxidative stress and cumulative exposure to environmental pollutants in lactating mothers living in the Valencian Region (Spain).
Article Snippet: To widen our understanding of internal exposure to multiple chemicals and extract exposure-response associations from human biomonitoring (HBM) studies, the Exposure Load (EL) approach was used on data from the BETTERMILK project.. Urinary levels of biomarkers of exposure to several contaminant groups —polycyclic aromatic hydrocarbons (PAHs), pesticides, bisphenols, phthalates, parabens, acrylamide, and metals — were analyzed, together with urinary concentrations of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8OHdG) as a biomarker of oxidative stress-induced DNA damage.. Potential determinants of exposure, obtained through questionnaires, were cross-sectionally evaluated in Valencian breastfeeding mothers (year 2015, Spain).

Article Title: Altered Fibroblast Glutamine Metabolism Is Linked to the Severity of Cardiac Dysfunction in DCMA, a Mitochondrial Cardiomyopathy.
Article Snippet: .. A heatmap was generated with log2 transformed and normalized counts using pheatmap() function in RStudio. ..

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Transcriptional response of the epithelium to infection with the different PAO1 strains. ( a ) Schematic representation of the analysis. ( b ) Volcano plot showing the log 2 fold change and -log 10 adjusted p-value of all genes, when comparing the transcriptome of 2D organoids exposed to PAO1 WT or PAO1 ΔQS. ( c ) Volcano plot showing the Log 2 fold change and -log 10 adjusted p-value per gene comparing the transcriptome of 2D organoids exposed to PAO1 WT or unexposed controls. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). ( d ) Gene ontology enrichment analysis showing top 10 categories enriched in 2D organoids exposed to PAO1 WT. Left panel: Healthy organoid line. Right: CF organoid line. ( e ) Gene expression heat map of genes from “Response to lipopolysaccharide” GO term category (GO:0032496). Color code indicates culture condition (co-culture or mono-culture) and PAO1 genotype (WT, Δ pqsA or ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Figure Lengend Snippet: Transcriptional response of the epithelium to infection with the different PAO1 strains. ( a ) Schematic representation of the analysis. ( b ) Volcano plot showing the log 2 fold change and -log 10 adjusted p-value of all genes, when comparing the transcriptome of 2D organoids exposed to PAO1 WT or PAO1 ΔQS. ( c ) Volcano plot showing the Log 2 fold change and -log 10 adjusted p-value per gene comparing the transcriptome of 2D organoids exposed to PAO1 WT or unexposed controls. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). ( d ) Gene ontology enrichment analysis showing top 10 categories enriched in 2D organoids exposed to PAO1 WT. Left panel: Healthy organoid line. Right: CF organoid line. ( e ) Gene expression heat map of genes from “Response to lipopolysaccharide” GO term category (GO:0032496). Color code indicates culture condition (co-culture or mono-culture) and PAO1 genotype (WT, Δ pqsA or ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Techniques: Infection, Gene Expression, Co-Culture Assay

Transcriptional response of PAO1 to the presence of airway epithelium. ( a ) Schematic representation of the analysis. ( b ) Volcano plot displaying the Log 2 fold change and –log 10 adjusted p-value of all genes, when comparing the PAO1 transcriptomes of co-culture and bacterial mono-culture samples. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). The number of genes upregulated in co-culture and bacterial mono-culture is indicated. ( c ) Gene ontology enrichment analysis showing top 10 categories enriched in PAO1 exposed to airway epithelium in co-culture. ( d ) Normalized count plots of genes involved in CCR pathway, crc and crcZ . ( e ) KEGG pathway pae00910 plot displaying the log 2 fold change of genes involved in denitrification . DEGs from co-culture vs. bacterial culture mono-culture comparison of PAO1 transcriptomes. ( f ) Normalized count plots of genes involved in P. aeruginosa antibiotic resistance. ( g ) Heat map displaying expression of genes involved in P. aeruginosa T6SS. Genes grouped by H1, H2 or H3 T6SS subtype , . Samples grouped by culture condition. Color code indicates culture condition (Green: bacterial mono-culture; magenta: co-culture) and PAO1 genotype (Dark: WT; middle: Δ pqsA ; light: ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Figure Lengend Snippet: Transcriptional response of PAO1 to the presence of airway epithelium. ( a ) Schematic representation of the analysis. ( b ) Volcano plot displaying the Log 2 fold change and –log 10 adjusted p-value of all genes, when comparing the PAO1 transcriptomes of co-culture and bacterial mono-culture samples. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). The number of genes upregulated in co-culture and bacterial mono-culture is indicated. ( c ) Gene ontology enrichment analysis showing top 10 categories enriched in PAO1 exposed to airway epithelium in co-culture. ( d ) Normalized count plots of genes involved in CCR pathway, crc and crcZ . ( e ) KEGG pathway pae00910 plot displaying the log 2 fold change of genes involved in denitrification . DEGs from co-culture vs. bacterial culture mono-culture comparison of PAO1 transcriptomes. ( f ) Normalized count plots of genes involved in P. aeruginosa antibiotic resistance. ( g ) Heat map displaying expression of genes involved in P. aeruginosa T6SS. Genes grouped by H1, H2 or H3 T6SS subtype , . Samples grouped by culture condition. Color code indicates culture condition (Green: bacterial mono-culture; magenta: co-culture) and PAO1 genotype (Dark: WT; middle: Δ pqsA ; light: ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Techniques: Co-Culture Assay, Comparison, Expressing

Epithelial effect on PAO1 QS regulation. ( a ) Gene expression heat map of genes involved in PQS, Las or Rhl QS pathways. ( b ) Volcano plots displaying gene log 2 fold change and –log 10 adjusted p-value when comparing the transcriptomes of WT and Δ pqsA PAO1 to those of ΔQS in co-culture (top) and in pure bacterial cultures (bottom). Venn diagrams display the overlap between genes up (right) and downregulated (left) in the comparisons. ( c ) Gene ontology enrichment analysis showing top 10 categories enriched in genes that are specifically upregulated in co-culture in WT and Δ pqsA PAO1 transcriptomes compared to ΔQS. ( d ) Gene expression heat map showing top 50 co-culture-specific DEGs. Genes are color-coded according to the following categories (Yellow: T6SS; purple: T2SS; green: Leucine metabolism; red: other pathways). ( e ) Gene expression heat map of T6SS eukaryotic and prokaryotic effectors. Sample color code indicates culture condition (Green: bacterial culture mono-culture; magenta: co-culture) and PAO1 genotype (Dark: WT; middle: Δ pqsA ; light: ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio.

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Figure Lengend Snippet: Epithelial effect on PAO1 QS regulation. ( a ) Gene expression heat map of genes involved in PQS, Las or Rhl QS pathways. ( b ) Volcano plots displaying gene log 2 fold change and –log 10 adjusted p-value when comparing the transcriptomes of WT and Δ pqsA PAO1 to those of ΔQS in co-culture (top) and in pure bacterial cultures (bottom). Venn diagrams display the overlap between genes up (right) and downregulated (left) in the comparisons. ( c ) Gene ontology enrichment analysis showing top 10 categories enriched in genes that are specifically upregulated in co-culture in WT and Δ pqsA PAO1 transcriptomes compared to ΔQS. ( d ) Gene expression heat map showing top 50 co-culture-specific DEGs. Genes are color-coded according to the following categories (Yellow: T6SS; purple: T2SS; green: Leucine metabolism; red: other pathways). ( e ) Gene expression heat map of T6SS eukaryotic and prokaryotic effectors. Sample color code indicates culture condition (Green: bacterial culture mono-culture; magenta: co-culture) and PAO1 genotype (Dark: WT; middle: Δ pqsA ; light: ΔQS). Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio.

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Techniques: Gene Expression, Co-Culture Assay

Benchmarking co-culture model with in vivo P. aeruginosa transcriptomic datasets directly isolated from the airways of CF subjects. ( a ) Accuracy analysis using gene-wise mean and standard deviation values from in vivo samples in Lewin et al., 2023 as reference. Genes were considered accurate if their expression was within 2 standard deviations of the mean in the in vivo sample. ( b ) PCA plots showing sample distribution by condition (Magenta: co-culture; green: bacterial culture in isolates; purple: in vivo) or by study of origin (Orange: this study; purple: Cornforth et al., 2018 ; pink: Kordes et al., 2019 ; blue: Rossi et al., 2018 ). ( c ) Volcano plots displaying gene log 2 fold change and -log 10 adjusted p-value comparing transcriptomes of in vivo P. aeruginosa (left) or co-cultured PAO1 (right) to those of all pure bacterial culture samples. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). Indicated in the boxes the number of up- or downregulated DEGs. ( d ) Venn diagrams displaying the overlap between genes that are upregulated (left), downregulated (middle), or both (right) in the previous in vivo and co-culture comparison to in vitro and mono-culture samples (b). ( e ) Expression heat map displaying the common up-(left) and downregulated (right) genes. Samples clustered based on the expression of all genes plotted per heat map. Color-code indicates condition (Magenta: co-culture; green: pure bacteria; purple: in vivo) and study of origin (Orange: this study; purple: Cornforth et al., 2018; pink: Kordes et al., 2019; blue: Rossi et al., 2018). Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture. Each node represents a protein encoded by a DEG. Edges represent known protein-protein association (either physical or functional) with a confidence level higher than 0.7. Node color represent clusters generated MCL method. Highlighted the pathway to which the cluster proteins belong. ( g ) Log 2 normalized count plots of representative genes from pathways highlighted by the network analysis. Color-code indicates Magenta: co-culture, green: pure bacteria and purple: in vivo.

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Figure Lengend Snippet: Benchmarking co-culture model with in vivo P. aeruginosa transcriptomic datasets directly isolated from the airways of CF subjects. ( a ) Accuracy analysis using gene-wise mean and standard deviation values from in vivo samples in Lewin et al., 2023 as reference. Genes were considered accurate if their expression was within 2 standard deviations of the mean in the in vivo sample. ( b ) PCA plots showing sample distribution by condition (Magenta: co-culture; green: bacterial culture in isolates; purple: in vivo) or by study of origin (Orange: this study; purple: Cornforth et al., 2018 ; pink: Kordes et al., 2019 ; blue: Rossi et al., 2018 ). ( c ) Volcano plots displaying gene log 2 fold change and -log 10 adjusted p-value comparing transcriptomes of in vivo P. aeruginosa (left) or co-cultured PAO1 (right) to those of all pure bacterial culture samples. Green indicates differentially expressed genes (DEGs) (log 2 fold change > 1 and adjusted p value < 0.05). Indicated in the boxes the number of up- or downregulated DEGs. ( d ) Venn diagrams displaying the overlap between genes that are upregulated (left), downregulated (middle), or both (right) in the previous in vivo and co-culture comparison to in vitro and mono-culture samples (b). ( e ) Expression heat map displaying the common up-(left) and downregulated (right) genes. Samples clustered based on the expression of all genes plotted per heat map. Color-code indicates condition (Magenta: co-culture; green: pure bacteria; purple: in vivo) and study of origin (Orange: this study; purple: Cornforth et al., 2018; pink: Kordes et al., 2019; blue: Rossi et al., 2018). Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture. Each node represents a protein encoded by a DEG. Edges represent known protein-protein association (either physical or functional) with a confidence level higher than 0.7. Node color represent clusters generated MCL method. Highlighted the pathway to which the cluster proteins belong. ( g ) Log 2 normalized count plots of representative genes from pathways highlighted by the network analysis. Color-code indicates Magenta: co-culture, green: pure bacteria and purple: in vivo.

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 79 (version 1.36.0) in Rstudio.

Techniques: Co-Culture Assay, In Vivo, Isolation, Standard Deviation, Expressing, Cell Culture, Comparison, In Vitro, Bacteria, Functional Assay, Generated

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture.

Techniques: Infection, Gene Expression, Co-Culture Assay

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture.

Techniques: Co-Culture Assay, Comparison, Expressing

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture.

Techniques: Gene Expression, Co-Culture Assay

Journal: Scientific Reports

Article Title: Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

doi: 10.1038/s41598-024-82500-w

Article Snippet: Heatmaps were plotted using the pheatmap function of DESeq2 (version 1.36.0) in Rstudio. ( f ) Protein-protein interaction network of common DEGs (in vivo and co-culture.

Techniques: Co-Culture Assay, In Vivo, Isolation, Standard Deviation, Expressing, Cell Culture, Comparison, In Vitro, Bacteria, Functional Assay, Generated

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