Package index • carnation

All functions

add.set.column(): Add set column to UpSet plot matrix

add_metadata(): Add metadata to counts data frame

alluvialServer(): Alluvial plot server function

alluvialUI(): Alluvial plot UI

check_user_access(): Get data areas a user has access to

cnetPlotServer(): Cnetplot server function

cnetPlotUI(): Cnetplot UI

create_access_yaml(): Create access yaml

dendrogramServer(): Dendrogram plot server function

dendrogramUI(): Dendrogram plot UI

distillPlotServer(): Distill enrichment plot server function

distillPlotUI(): Distill enrichment plot UI

downloadButtonServer(): Download button module server

downloadButtonUI(): Download button module ui

enrichServer(): Functional enrichment module server function

enrichUI(): Functional enrichment module UI

enrich_to_genetonic(): Convert enrichResult to GeneTonic object

enrichmapServer(): Enrichment map plot server function

enrichmapUI(): Enrichment map plot UI

format_genes(): format gene names to look pretty in table output

fromList.with.names(): Prepare list for UpSet plots, but include rownames

fuzzyPlotServer(): Fuzzy enrichment plot server function

fuzzyPlotUI(): Fuzzy enrichment plot UI

genePlotServer(): Gene plot module server function

genePlotUI(): Gene plot module UI

get_access_path(): Get path to access yaml file

get_common_path_from_list(): Return common base path from list of paths

get_config(): Get config

get_degplot(): Plot a degPatterns object

get_gene_counts(): Get read counts for gene

get_project_name_from_path(): Get project name from path

get_y_init(): Get initial y-axis limits

getcountplot(): Create gene plot

gs_radar(): Radar plot

heatmapServer(): Heatmap module server function

heatmapUI(): Heatmap module UI

helpButtonServer(): Help button module server

helpButtonUI(): Help button module ui

helpModal(): Help modal

horizonServer(): Horizon plot server function

horizonUI(): Horizon plot UI

in_admin_group(): is user is in admin group?

install_carnation(): Create carnation python environment

is_site_admin(): is user an admin?

loadDataServer(): Load data module server function

loadDataUI(): Load data module UI

maPlotServer(): MA plot module server function

maPlotUI(): MA plot module UI

makeEnrichResult(): Make an enrichResult obj from a data frame

make_final_object(): Make final object for internal use by the app

metadataServer(): Metadata module server

metadataUI(): Metadata module ui

my.summary(): Summarize DESeq2 results into a dataframe

patternPlotServer(): Pattern plot module server function

patternPlotUI(): Pattern plot module UI

pcaPlotServer(): PCA plot module server function

pcaPlotUI(): PCA plot module UI

plotMA.label(): Create a labeled MA plot

plotMA.label_ly(): Create an interactive labeled MA plot

plotPCA.ly(): Plot an interactive PCA plot

plotPCA.san(): Adjustable PCA plot

plotScatter.label(): Plot a scatterplot to compare two contrasts

plotScatter.label_ly(): Plot an interactive scatterplot to compare two contrasts

radarServer(): Radar plot server function

radarUI(): Radar plot UI

read_access_yaml(): Read access yaml with user groups and data areas

run_carnation(): Carnation

saveServer(): Save object module server function

saveUI(): Save object module UI

save_access_yaml(): Save access yaml to file

scatterPlotServer(): Scatterplot module server function

scatterPlotUI(): Scatterplot module UI

settingsServer(): Settings module server

settingsUI(): Settings module ui

summarize.res.list(): Combine everything in the results list into a single table

sumovPlotServer(): Summary overview plot server function

sumovPlotUI(): Summary overview plot ui

top.genes(): Get top DE genes by log2FoldChange or adjusted p-value

upsetPlotServer(): Upset plot module server function

upsetPlotUI(): Upset plot module UI