Package index • plotomics

Expression and abundance

Differential expression, expression matrices and per-feature distributions. Each constructor returns an htmlwidget.

volcano(): Volcano plot
bioheatmap() heatmap_plotomics(): Expression heatmap
clustermap(): Clustered heatmap with dendrograms
dotplot(): Marker gene dot plot
violin(): Stacked violin plot

Single-cell and spatial

Dimensionality-reduction maps and measurements placed on tissue.

embedding(): Embedding scatter (UMAP / t-SNE / PCA)
spatial(): Spatial map over a tissue image

Cohort and variant genomics

Alteration landscapes, variant positions, survival and signature profiles.

oncoplot(): Oncoplot (OncoPrint)
lollipop(): Protein domain lollipop
km(): Kaplan-Meier survival curves with a number-at-risk table
profile(): Grouped categorical bar profile

Sets, hierarchies and networks

Set intersections, hierarchical composition and large graphs.

upset(): UpSet plot of set intersections
treemap(): Gene / pathway treemap
network(): Network graph

Genome and chromatin

Contact matrices and track-based genome browsers.

hic(): Hi-C contact matrix
igv(): Genome viewer (igv.js)
gosling(): Declarative genomics figures (Gosling.js)

Data helpers

Precompute the inputs the widgets consume. The widgets draw, they do not estimate, so these run the statistics in R where you can see them.

oncoplot_memo_sort(): Conventional oncoplot row and column ordering
upset_intersections(): Exclusive set intersections from a membership matrix
violin_density(): Kernel densities on a shared grid

Shiny bindings

Output and render pairs for use in classic Shiny apps.

bioheatmapOutput() renderBioheatmap(): Shiny bindings for bioheatmap
clustermapOutput() renderClustermap(): Shiny bindings for clustermap
dotplotOutput() renderDotplot(): Shiny bindings for dotplot
embeddingOutput() renderEmbedding(): Shiny bindings for embedding
goslingOutput() renderGosling(): Shiny bindings for gosling
hicOutput() renderHic(): Shiny bindings for hic
igvOutput() renderIgv(): Shiny bindings for igv
kmOutput() renderKm(): Shiny bindings for km
lollipopOutput() renderLollipop(): Shiny bindings for lollipop
networkOutput() renderNetwork(): Shiny bindings for network
oncoplotOutput() renderOncoplot(): Shiny bindings for oncoplot
profileOutput() renderProfile(): Shiny bindings for profile
spatialOutput() renderSpatial(): Shiny bindings for spatial
treemapOutput() renderTreemap(): Shiny bindings for treemap
upsetOutput() renderUpset(): Shiny bindings for upset
violinOutput() renderViolin(): Shiny bindings for violin
volcanoOutput() renderVolcano(): Shiny bindings for volcano