Man pages for jdreyf/ezlimmaplot
Bioinformatics plots using limma and ggplot2, some from output of ezlimma
| barplot_pwys | Make barplots for the p-Values of Pathway Analysis |
| bubbleplot_pwys | Make bubble plots for the significance, DE proportion, and... |
| dotplot_pwys | Make dot plots for the significance and DE proportion of... |
| edgelist2graph | Transform a data frame edge list into an 'igraph' graph |
| extract_prefix | Extract prefix from names |
| ezheat | Plot heatmap |
| ezpca | PCA plot of top two components |
| eztsne | tSNE plot of first two dimensions |
| ezvenn | Venn diagrams |
| ezvolcano | Volcano plot |
| multi_cor_heat | Plot one heatmap per phenotype correlation |
| multi_covar_pca | PCA plots of top two components colored by each covariate |
| multi_heat | Plot one heatmap per comparison |
| multi_venn | Multiple Venn diagrams |
| multi_volcano | Multiple volcano plots |
| neighbor_nms | Get names of nodes' neighbors |
| order_stats_by_alternative | Order values based on alternative hypothesis |
| pivot_roast_longer | Lengthen output table from 'ezlimma::roast_*' to be plotted... |
| plot_by_grp | Make box, dot, violin or bar plots for a feature per group |
| plot_man | Plot mediation exposure, mediator, and outcome per mediator |
| plot_missing | Plot missingness probability against average log abundance |
| plot_pwy | Plot network diagram for a pathway |
| prune_mat | Prune matrix |
| sif2edgelist | Clean Pathway Commons SIF file |
| signif_hist | Plot histograms of significance (p-value & FDR) columns |
| sub_labels | Replace names with non-missing label.v |
