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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'
ClusterLabels(x)

# S4 method for class 'MemPlotFolio'
ClusterLabels(x) <- value

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

# S4 method for class 'MemPlotFolio'
ClusterData(x) <- value

# 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, legend_x = "bottomleft", legend_y = NULL, ...)

# S4 method for class 'MemPlotFolio'
CnetExemplar(
  x,
  num,
  do_plot,
  legend_x = "bottomleft",
  legend_y = NULL,
  main = NULL,
  ...
)

# S4 method for class 'MemPlotFolio'
CnetCluster(
  x,
  cluster,
  do_plot,
  legend_x = "bottomleft",
  legend_y = NULL,
  main = NULL,
  ...
)

# S4 method for class 'MemPlotFolio,ANY'
plot(x, y, ...)

# S4 method for class 'MemPlotFolio'
EnrichmentMap(
  x,
  do_plot = TRUE,
  legend_x = "bottomleft",
  legend_y = NULL,
  params = list(),
  ...
)

Arguments

mpf

list output from mem_plot_folio()

x

MemPlotFolio object

...

additional arguments passed to plot_mpf()

value

named character vector of cluster labels, where names correspond to cluster names as returned by Clusters(x).

y

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.

ClusterLabels(MemPlotFolio) returns a named character vector of cluster labels, or NULL if none are defined.

ClusterLabels<-(MemPlotFolio) returns the updated MemPlotFolio object with new cluster labels stored in metadata$cluster_labels.

ClusterData(MemPlotFolio) returns a named list of cluster data, or NULL if none are defined.

ClusterData<-(MemPlotFolio) returns the updated MemPlotFolio object with new cluster data stored in metadata$cluster_data.

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), in addition to rendering the heatmap. It returns ComplexHeatmap::Heatmap when do_plot is FALSE, containing enrichment P-values by enrichment, and pathway rows in clusters. Optional arguments '...' include:

  • 'main' or 'column_title' for overall plot title;

  • 'column_title_gp' as grid::gpar() to adjust title font;

  • 'use_cluster_labels' logical whether to use ClusterLabels() as row title entries.

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. The legend position can be adjusted using 'legend_x', 'legend_y' which are passed to mem_legend() as 'x' and 'y'.

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.

  • ClusterLabels(MemPlotFolio): Returns cluster labels stored in the metadata slot of MemPlotFolio.

  • ClusterLabels(MemPlotFolio) <- value: Sets cluster labels in the metadata slot of MemPlotFolio.

  • ClusterData(MemPlotFolio): Returns cluster data stored in the metadata slot of MemPlotFolio, intended to store further information to describe each cluster.

  • ClusterData(MemPlotFolio) <- value: Sets cluster data in the metadata slot of MemPlotFolio, intended to store further information to describe each cluster. It should be the same length as Clusters(x) and have no names, or have names equal to names(Clusters(x)).

  • 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. Optional arguments '...' include:

    • 'main' or 'column_title' for overall plot title;

    • 'column_title_gp' as grid::gpar() to adjust title font;

    • 'use_cluster_labels' logical whether to use ClusterLabels() as row title entries.

  • 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. When 'type' is not defined: it uses type='cluster' if ClusterLabels() is defined, otherwise type='set'; then it appends '2' to the end if there are more than 1000 nodes. Argument 'type' can be:

    • type='title' or type='' to use cluster title

    • type='set' to use abbreviated pathway names

    • type='cluster' to use cluster labels

    • type='attribute' to use any existing vertex attribute.

    • Append '2' to the end to hide gene labels. For example type='set2'.

    Recognized arguments in '...':

    • 'width' to apply word-wrap to cluster labels, or vertex attribute.

    • 'maxNchar' to set maximum string character length, passed to fixSetLabels().

    • 'layout' passed to set_igraph_layout(cnet, layout) to update the node layout.

    • 'rotate_degrees' with numeric value. When set, it calls rotate_igraph_layout() with defaults.

    • All other '...' arguments are passed to jam_igraph().

    The legend includes direction if encoded in the 'MemPlotFolio', but can be forced with do_directional=TRUE or FALSE.

  • 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.

    The legend includes direction if encoded in the 'MemPlotFolio', but can be forced with do_directional=TRUE or FALSE. Legend position is controlled by legend_x,legend_y, default legend_x="bottomleft".

  • 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.

    The legend includes direction if encoded in the 'MemPlotFolio', but can be forced with do_directional=TRUE or FALSE. Plot title 'main', default NULL uses the cluster label if present, then cluster name. Use main=FALSE or main="" to hide the title.

  • plot(x = MemPlotFolio, y = ANY): Plot a MemPlotFolio object calling plot_mpf()

  • EnrichmentMap(MemPlotFolio): EnrichmentMap igraph network to connect pathway gene sets based upon Jaccard overlap between each pathway pair. Note '...' arguments are passed to jam_igraph() and mem_legend() when do_plot=TRUE. Argument 'params' is a list with additional arguments: 'repulse', 'width', 'group', 'mark.expand', 'do_legend'.

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'")