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Enrichment Map/Network

Source: R/enrich.R
enrichmap1.Rd

PrepareEnrichrResult is a function to process the enrichment results from Enrichr. EnrichMap is a function to plot the enrichment map. EnrichNetwork is a function to plot the enrichment network.

Usage

PrepareEnrichrResult(data, n_input = NULL)

EnrichMap(
  data,
  split_by = NULL,
  split_by_sep = "_",
  top_term = 10,
  metric = "p.adjust",
  layout = "fr",
  minchar = 2,
  cluster = "fast_greedy",
  show_keyword = FALSE,
  nlabel = 4,
  character_width = 50,
  mark = "ellipse",
  label = c("term", "feature"),
  labelsize = 5,
  expand = c(0.4, 0.4),
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...
)

EnrichNetwork(
  data,
  split_by = NULL,
  split_by_sep = "_",
  top_term = 10,
  metric = "p.adjust",
  character_width = 50,
  layout = "fr",
  layoutadjust = TRUE,
  adjscale = 60,
  adjiter = 100,
  blendmode = "blend",
  labelsize = 5,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...
)

Arguments

data

A data frame containing the data to be plotted. It should be in the format of clusterProfiler enrichment result, which includes the columns: ID, Description, GeneRatio, BgRatio, pvalue, p.adjust, qvalue, geneID and Count.

  • The ID, qvalue and Count columns are optional.

  • The Description is the description of the term.

  • The GeneRatio is the number of genes in the term divided by the total number of genes in the input list.

  • The BgRatio is the number of genes in the term divided by the total number of genes in the background list (all terms).

  • The Count column, if given, should be the same as the first number in GeneRatio.

If you have enrichment results from multiple databases, you can combine them into one data frame and add a column (e.g. Database) to indicate the database. You can plot them in a single plot using the split_by argument (e.g. split_by = "Database").

n_input

An integer specifying the number of input genes. Enrichr result doesn't ship with the number of input genes. You can either provide the number directly or we will infer it. See details.

split_by

The column(s) to split data by and plot separately.

split_by_sep

The separator for multiple split_by columns. See split_by

top_term

An integer specifying the number of top terms to show.

metric

A character string specifying the metric to use for the size of the nodes. It is also used to order the terms when selected the top terms. Either "pvalue" or "p.adjust". The default is "p.adjust".

layout

A character string specifying the layout of the graph. Either "circle", "tree", "grid" or other layout functions in igraph.

minchar

An integer specifying the minimum number of characters to show in the keyword.

cluster

A character string specifying the clustering method. Either "fast_greedy", "walktrap", "edge_betweenness", "infomap" or other clustering functions in igraph.

show_keyword

A logical value specifying whether to show the keyword instead of Description/Term in the plot.

nlabel

An integer specifying the number of labels to show in each cluster.

character_width

The width of the characters used to wrap the keyword.

mark

A character string specifying the mark to use for the nodes. Either "ellipse", "rect", "circle", "text" or other mark functions in ggforce.

label

A character string specifying the label to show in the legend. Either "term" or "feature". The default is "term".

labelsize

A numeric value specifying the size of the label.

expand

The values to expand the x and y axes. It is like CSS padding. When a single value is provided, it is used for both axes on both sides. When two values are provided, the first value is used for the top/bottom side and the second value is used for the left/right side. When three values are provided, the first value is used for the top side, the second value is used for the left/right side, and the third value is used for the bottom side. When four values are provided, the values are used for the top, right, bottom, and left sides, respectively. You can also use a named vector to specify the values for each side. When the axis is discrete, the values will be applied as 'add' to the 'expansion' function. When the axis is continuous, the values will be applied as 'mult' to the 'expansion' function. See also https://ggplot2.tidyverse.org/reference/expansion.html

theme

A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".

theme_args

A list of arguments to pass to the theme function.

palette

A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.

palcolor

A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).

alpha

A numeric value specifying the transparency of the plot.

aspect.ratio

A numeric value specifying the aspect ratio of the plot.

legend.position

A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".

legend.direction

A character string specifying the direction of the legend.

title

A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.

subtitle

A character string specifying the subtitle of the plot.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

seed

The random seed to use. Default is 8525.

combine

Whether to combine the plots into one when facet is FALSE. Default is TRUE.

nrow

A numeric value specifying the number of rows in the facet.

ncol

A numeric value specifying the number of columns in the facet.

byrow

A logical value indicating whether to fill the plots by row.

...

Additional arguments.

layoutadjust

A logical value specifying whether to adjust the layout of the network.

adjscale

A numeric value specifying the scale of the adjustment.

adjiter

A numeric value specifying the number of iterations for the adjustment.

blendmode

A character string specifying the blend mode of the colors. Either "blend", "average", "multiply" and "screen".

Value

A data frame that can be used in EnrichMap.

A ggplot object or wrap_plots object or a list of ggplot objects

Details

In order to use the EnrichMap and EnrichNetwork functions and other visualization functions in plotthis, the enrichment results from Enrichr need to be processed by the PrepareEnrichrResult function. The following columns are renamed:

  • Term -> Description

  • Genes -> geneID (separated replaced by /)

  • P.value -> pvalue

  • Adjusted.P.value -> p.adjust Additionally, GeneRatio and BgRatio columns are inferred. From enrichr's documentation, the oddsRatio is defined as: oddsRatio = (A * (D - B - C + A) / max((B - A) * (C - A), 1), where A is the overlapping genes; B is the total genes in the gene set; C (n_input) is the genes in input list; D is the total genes in the background. D is not provided by Enrichr. To infer it, D = oddsRatio * max((B - A) * (C - A), 1) / A + B + C - A.

  • Overlap = A / B (from Enrichr)

  • GeneRatio = A / C (from ClusterProfiler)

  • BgRatio = B / D (from ClusterProfiler) C (n_input), if not provided, will be inferred when D for all terms are equal. When starting inferrence, the minimum value to try will be unique genes in data$Genes/data$geneID.

Examples

data(enrich_example)
EnrichMap(enrich_example)

EnrichMap(enrich_example, label = "feature")

EnrichMap(enrich_example, show_keyword = TRUE, label = "term")

EnrichMap(enrich_example, show_keyword = TRUE, label = "feature")


data(enrich_multidb_example)
EnrichMap(enrich_multidb_example, split_by = "Database")

EnrichMap(enrich_multidb_example, split_by = "Database",
          palette = list(DB1 = "Paired", DB2 = "Set1"))

EnrichNetwork(enrich_example, top_term = 5)