Transcriptome Visualization Process Scheme

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Documentation for package ‘TOmicsVis’ version 2.0.0

Help Pages

box_plot Box plot support two levels and multiple groups with P value.
chord_plot Chord plot for visualizing the relationships of pathways and genes.
circos_heatmap Circos heatmap plot for visualizing gene expressing in multiple samples.
corr_heatmap Correlation Heatmap for samples/groups based on Pearson algorithm.
degs_lists Paired comparisons differentially expressed genes (degs) among groups.
degs_stats All DEGs of paired comparison CT-vs-LT12 stats dataframe.
degs_stats2 All DEGs of paired comparison CT-vs-LT12 stats2 dataframe.
dendro_plot Dendrograms for multiple samples/groups clustering.
flower_plot Flower plot for stat common and unique gene among multiple sets.
gene_cluster_trend Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.
gene_expression All genes in all samples expression dataframe of RNA-Seq.
gene_expression2 Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq.
gene_expression3 Shared DEGs of all paired comparisons in all groups expression dataframe of RNA-Seq.
gene_go_kegg GO and KEGG annotation of background genes.
gene_go_kegg2 GO and KEGG annotation of background genes.
gene_rank_plot Gene ranking dotplot for visualizing differentailly expressed genes.
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.
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 from WGCNA tan module top-200 dataframe.
network_plot Network plot for analyzing and visualizing relationship of genes.
pca_analysis PCA dimensional reduction analysis for RNA-Seq.
pca_plot PCA dimensional reduction visualization for RNA-Seq.
quantile_plot Quantile plot for visualizing data distribution.
samples_groups Samples and groups for gene expression.
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_filter Table filter used to filter row by column condition.
table_merge Table merge used to merge multiple variables to on variable.
table_split Table split used for splitting a grouped column to multiple columns.
tomicsvis TOmicsVis shiny app start function.
traits_sex Length, Width, Weight, and Sex traits dataframe.
trend_plot Trend plot for visualizing gene expression trend profile in multiple traits.
tsne_analysis TSNE analysis for analyzing and visualizing TSNE algorithm.
tsne_plot TSNE plot for analyzing and visualizing TSNE algorithm.
umap_analysis UMAP analysis for analyzing RNA-Seq data.
umap_plot UMAP plot for analyzing and visualizing UMAP algorithm.
upsetr_plot UpSet plot for stat common and unique gene among multiple 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.
weight_sex Weight and Sex traits dataframe.
wgcna_pipeline WGCNA analysis pipeline for RNA-Seq.