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Mem S4 class, accessors, getters, and setters

Source: R/AllClasses.R, R/methods-MemPlotFolio.R
MemPlotFolio-class.Rd

Mem class containing results from multiEnrichMap(), current class version "1.0.0".

Usage

list_to_MemPlotFolio(mpf)

MemPlotFolio_to_list(x, ...)

# S4 method for class 'MemPlotFolio'
show(object)

# S4 method for class 'MemPlotFolio'
Clusters(x)

# S4 method for class 'MemPlotFolio'
GeneClusters(x)

# S4 method for class 'MemPlotFolio'
thresholds(x)

# S4 method for class 'MemPlotFolio'
metadata(x)

# S4 method for class 'MemPlotFolio'
Caption(x, ...)

# S4 method for class 'MemPlotFolio'
CaptionLegendList(x, ...)

# S4 method for class 'MemPlotFolio'
EnrichmentHeatmap(x, do_plot, ...)

# S4 method for class 'MemPlotFolio'
GenePathHeatmap(x, do_plot, ...)

# S4 method for class 'MemPlotFolio'
CnetCollapsed(x, type, do_plot, ...)

# S4 method for class 'MemPlotFolio'
CnetExemplar(x, num, do_plot, ...)

# S4 method for class 'MemPlotFolio'
CnetCluster(x, cluster, do_plot, ...)

Arguments

mpf

list output from mem_plot_folio()

x

MemPlotFolio object

...

additional arguments are ignored

Value

list_to_MemPlotFolio() returns a MemPlotFolio S4 object, from 'list' or 'MemPlotFolio' input.

MemPlotFolio_to_list() returns a list

Clusters(MemPlotFolio) returns a list of character vectors, named by cluster.

GeneClusters(MemPlotFolio) returns a list of character vectors, named by cluster.

thresholds(MemPlotFolio) returns a list of thresholds used with mem_plot_folio().

metadata(MemPlotFolio) returns a list of metadata used with mem_plot_folio().

metadata(MemPlotFolio) returns a character string with caption summary used with mem_plot_folio(). Multiple lines are delimited by newline characters.

metadata(MemPlotFolio) returns the caption summary in the form of ComplexHeatmap::Legends suitable to draw() as R grid graphics.

EnrichmentHeatmap(MemPlotFolio) returns a ComplexHeatmap::HeatmapList when do_plot is TRUE (default), ComplexHeatmap::Heatmap when do_plot is FALSE, containing enrichment P-values by enrichment, and pathway rows in clusters.

GenePathHeatmap(MemPlotFolio) returns a ComplexHeatmap::HeatmapList when do_plot is TRUE (default), ComplexHeatmap::Heatmap when do_plot is FALSE, containing the genes-pathways incidence matrix and associated caption.

CnetCollapsed(MemPlotFolio) returns an igraph object invisibly, with Gene and Set nodes representing the collapsed pathway clusters.

CnetExemplar(MemPlotFolio) returns an igraph object with Gene and Set nodes for the 'num' number of exemplars per cluster.

CnetCluster(MemPlotFolio) returns an igraph object invisibly, using all pathways in the cluster defined with argument cluster.

Functions

  • list_to_MemPlotFolio(): Convert legacy list to S4 MemPlotFolio

  • MemPlotFolio_to_list(): Coerce S4 MemPlotFolio to list format

  • show(MemPlotFolio): Show summary of a MemPlotFolio object, dimensions defined by genes, sets, enrichments.

  • Clusters(MemPlotFolio): Returns the order of gene sets from MemPlotFolio results as a list named by pathway cluster, containing character vectors of pathway gene sets.

  • GeneClusters(MemPlotFolio): Returns the order of genes from MemPlotFolio results as a list named by gene cluster, containing character vectors of genes.

  • thresholds(MemPlotFolio): Returns the thresholds used with MemPlotFolio.

  • metadata(MemPlotFolio): Returns the metadata used with MemPlotFolio.

  • Caption(MemPlotFolio): Returns the caption summary for MemPlotFolio.

  • CaptionLegendList(MemPlotFolio): Returns the caption summary for MemPlotFolio as ComplexHeatmap::Legends.

  • EnrichmentHeatmap(MemPlotFolio): Draws the enrichment heatmap from MemPlotFolio results.

  • GenePathHeatmap(MemPlotFolio): Draws the gene-pathway set heatmap from MemPlotFolio results.

  • CnetCollapsed(MemPlotFolio): Draws the Cnet collapsed network from MemPlotFolio results. Note that '...' arguments are passed to jam_igraph() and mem_legend() when do_plot=TRUE. Argument type can be:

    • type='' (default) to use cluster title

    • type='set' to use abbreviated pathway names

    • type='set2' to use abbreviated pathway names, with hidden gene labels

  • CnetExemplar(MemPlotFolio): Draws the Cnet exemplar network from MemPlotFolio results for 'num' exemplar per cluster. Note that '...' arguments are passed to jam_igraph() and mem_legend() when do_plot=TRUE.

  • CnetCluster(MemPlotFolio): Draws the Cnet network from MemPlotFolio results for a specific cluster. Note that '...' arguments are passed to jam_igraph() and mem_legend() when do_plot=TRUE.

See also

Other jam Mem utilities: Mem-class, fixSetLabels(), mem2cnet(), mem2emap()

Other MemPlotFolio: check_MemPlotFolio(), score_gene_path_clusters()

Examples

# list_to_MemPlotFolio examples
data(Memtest)
mpf <- mem_plot_folio(Memtest, do_plot=FALSE,
   do_which=c(1, 2, 3, 4), returnType="list")
Mpf <- list_to_MemPlotFolio(mpf)

data(Memtest)
mpf <- mem_plot_folio(Memtest, do_plot=FALSE, returnType="list")
Mpf <- list_to_MemPlotFolio(mpf)

# enrichment heatmap
EnrichmentHeatmap(Mpf, column_title="Enrichment Heatmap")


# Gene-path heatmap
GenePathHeatmap(Mpf, column_title="Gene-Path Heatmap")


# Cnet collapsed sets
CnetCollapsed(Mpf, type="set", use_shadowText=TRUE, main="Cnet Collapsed Sets")


# Cnet exemplar plot
CnetExemplar(Mpf, num=2, use_shadowText=TRUE, main="Cnet Exemplars, num=2")


# Cnet cluster plot
CnetCluster(Mpf, cluster="B", use_shadowText=TRUE, main="Cnet Cluster 'B'")