Transcriptome Visualization Process Scheme


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Documentation for package ‘TOmicsVis’ version 1.2.3

Help Pages

box_data Box data for box_plot, include Value, Level1 and Level2 columns.
box_plot Box plot support two levels and multiple groups with P value.
chord_data Chord data as example data for the chord_plot function.
chord_plot Chord plot for visualizing the relationships of pathways and genes.
circos_heatmap Circos heatmap plot for visualizing gene expressing in multiple samples.
circos_heatmap_data Gene expression as example data for circos_heatmap function.
corr_heatmap Correlation Heatmap for samples/groups based on Pearson algorithm.
deg_data Differentially expressed genes (DEGs) for volcano_plot function.
deg_data2 Differentially expressed genes (DEGs) for ma_plot function.
dendro_plot Dendrograms for multiple samples/groups clustering.
flower_plot Flower plot for stat common and unique gene among multiple sets.
gene_cluster_data Gene cluster data for gene_cluster_trend function.
gene_cluster_trend Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.
gene_exp Gene Expression dataframe of RNA-Seq.
gene_exp2 Gene Expression dataframe of RNA-Seq.
gene_rank_plot Gene ranking dotplot for visualizing differentailly expressed genes.
go_anno GO annotation (BP, CC, MF) of genes as template data.
go_deg_fc GO deg (differentially expressed genes) and fc (fold change) template data.
go_enrich GO enrichment analysis based on GO annotation results (None/Exist Reference Genome).
go_enrich_bar GO enrichment analysis and bar plot (None/Exist Reference Genome).
go_enrich_dot GO enrichment analysis and dot plot (None/Exist Reference Genome).
go_enrich_net GO enrichment analysis and net plot (None/Exist Reference Genome).
go_enrich_stat GO enrichment analysis and stat plot (None/Exist Reference Genome).
heatmap_cluster Heatmap cluster for visualizing clustered gene expression data.
heatmap_group Heatmap group for visualizing grouped gene expression data.
heatmap_group_data Heatmap group data for heatmap_group function.
kegg_anno KEGG annotation (kegg_pathway) of genes as template data.
kegg_deg_fc KEGG deg (differentially expressed genes) and fc (fold change) template data.
kegg_enrich KEGG enrichment analysis based on KEGG annotation results (None/Exist Reference Genome).
kegg_enrich_bar KEGG enrichment analysis and bar plot (None/Exist Reference Genome).
kegg_enrich_dot KEGG enrichment analysis and dot plot (None/Exist Reference Genome).
kegg_enrich_net KEGG enrichment analysis and net plot (None/Exist Reference Genome).
ma_plot MversusA plot for visualizing differentially expressed genes.
network_data Network data as example for network_plot function.
network_plot Network plot for analyzing and visualizing relationship of genes.
pca_group_sample PCA data2 include groups and samples.
pca_plot PCA dimensional reduction visualization for RNA-Seq.
pca_sample_gene PCA data1 include samples and genes.
quantile_data Quantile data for quantile_plot example.
quantile_plot Quantile plot for visualizing data distribution.
survival_data Survival data as example data for survival_plot function.
survival_plot Survival plot for analyzing and visualizing survival data.
table_cross Table cross used to cross search and merge results in two tables.
table_cross_data1 Table cross data1 for table_cross function.
table_cross_data2 Table cross data2 for table_cross function.
table_filter Table filter used to filter row by column condition.
table_filter_data Table filter data as example for table_filter function.
table_merge Table merge used to merge multiple variables to on variable.
table_merge_data Table merge data as example for table_merge function.
table_split Table split used for splitting a grouped column to multiple columns.
table_split_data Table split data as example for table_split function.
trend_data Trend data include genes expression in multiple traits as example for trend_plot function.
trend_plot Trend plot for visualizing gene expression trend profile in multiple traits.
tsne_data TSNE data as example for tsne_plot function.
tsne_plot TSNE plot for analyzing and visualizing TSNE algorithm.
venn_data Venn data with multiple gene sets.
venn_plot Venn plot for stat common and unique gene among multiple sets.
violin_plot Violin plot support two levels and multiple groups with P value.
volcano_plot Volcano plot for visualizing differentailly expressed genes.
wgcna_gene_exp WGCNA gene expression data for wgcna_analysis.
wgcna_pipeline WGCNA analysis pipeline for RNA-Seq.
wgcna_sample_group WGCNA samples groups data for wgcna_analysis.