mem_enrichment_heatmap: MultiEnrichment Heatmap of enrichment P-values

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

MultiEnrichment Heatmap of enrichment P-values

Description

MultiEnrichment Heatmap of enrichment P-values

Usage

mem_enrichment_heatmap(
  mem,
  style = c("dotplot_inverted", "dotplot", "heatmap"),
  apply_direction = FALSE,
  p_cutoff = mem$p_cutoff,
  min_count = 1,
  p_floor = 1e-10,
  point_size_factor = 1,
  point_size_max = 8,
  point_size_min = 2,
  row_method = "euclidean",
  column_method = "euclidean",
  name = "-log10P",
  row_dend_reorder = TRUE,
  row_dend_width = grid::unit(30, "mm"),
  row_fontsize = NULL,
  row_cex = 1,
  row_split = NULL,
  row_gap = grid::unit(2, "mm"),
  cluster_rows = TRUE,
  column_fontsize = NULL,
  column_cex = 1,
  cluster_columns = FALSE,
  sets = NULL,
  color_by_column = FALSE,
  cex.axis = 1,
  lens = 3,
  cexCellnote = 1,
  column_title = NULL,
  row_names_max_width = grid::unit(300, "mm"),
  column_names_max_height = grid::unit(300, "mm"),
  heatmap_legend_param = NULL,
  hm_cell_size = NULL,
  legend_height = grid::unit(6, "cm"),
  legend_cex = 1,
  direction_cutoff = 0,
  gene_count_max = NULL,
  top_annotation = NULL,
  outline = TRUE,
  show_enrich = NULL,
  use_raster = FALSE,
  do_plot = TRUE,
  ...
)

Arguments

mem	list object created by multiEnrichMap(). Specifically the object is expected to contain enrichIM.
style	character string indicating the style of heatmap: "heatmap" produces a regular heatmap, shaded by log10(Pvalue); "dotplot" produces a dotplot, where the dot size is proportional to the number of genes. See function description for details on how to include the point size legend beside the heatmap. The main benefit of using "dotplot" style is that it also indicates the relative number of genes involved in the enrichment.
apply_direction	logical, default FALSE, whether to define a bivariate color scheme which uses mem$enrichIMdirection when defined. The color scheme is intended to indicate both the directional strength (usually with some type of z-score) and the statistical enrichment (usually with the enrichment P-value or adjusted P-value).
p_cutoff	numeric value of the enrichment P-value cutoff, by default this value is obtained from mem$p_cutoff to be consistent with the original multiEnrichMap() analysis. P-values above p_cutoff are not colored, and are therefore white. This behavior is intended to indicate pathways with P-value above this threshold did not meet the threshold, instead of pathways with similar P-values displaying with similar color.
min_count	numeric number of genes required for a pathway to be considered dysregulated.
p_floor	numeric minimum P-value used for the color gradient. P-values below this floor are colored with the maximum color gradient. This value is intended to be used in cases where one enrichment P-value is very low (e.g. 1e-36) to prevent all other P-values from being colored pale red-white and not be noticeable.
point_size_factor	numeric used to adjust the legend point size, since the heatmap point size is dependent upon the number of rows, the legend may require some manual adjustment to make sure the legend matches the heatmap.
point_size_min, point_size_max	numeric values which define the minimum and maximum point sizes, effectively defining the range permitted when style="dotplot".
row_method	character string of the distance method to use for row and column clustering. The clustering is performed by amap::hcluster().
name	character value passed to ComplexHeatmap::Heatmap(), used as a label above the heatmap color legend.
row_dend_reorder	logical indicating whether to reorder the row dendrogram using the method described in ComplexHeatmap::Heatmap(). The end result is minor reshuffling of leaf nodes on the dendrogram based upon mean signal in each row, which can sometimes look cleaner.
row_fontsize, column_fontsize	optional numeric arguments passed to ComplexHeatmap::Heatmap() to size row and column labels.
cluster_columns	logical indicating whether to cluster heatmap columns, by default columns are not clustered.
sets	character vector of sets (pathways) to include in the heatmap, all other sets will be excluded.
color_by_column	logical indicating whether to colorize the heatmap using mem$colorV as defined for each comparison. This option is currently experimental, and produces a base R heatmap using jamba::imageByColors().
cex.axis	numeric adjustment for axis labels, passed to jamba::imageByColors() only when color_by_column=TRUE.
lens	numeric value used in color gradients, defining the extent the color gradient is enhanced in the mid-ranges (positive lens), or diminished in the mid-ranges (negative lens). There is no quantitative standard measure for color gradient changes, so this option is intended to help adjust and improve the visual perception of the current data.
cexCellnote	numeric character expansion value used only when color_by_column=TRUE, used to adjust the P-value label size inside each heatmap cell.
column_title	optional character string with title to display above the heatmap.
row_names_max_width, column_names_max_height, heatmap_legend_param	arguments passed to ComplexHeatmap::Heatmap() and provided here for convenience.
hm_cell_size	grid::unit or numeric, default NULL, to define an optional fixed heatmap cell size, useful to define absolute square heatmap cells. When numeric it is interpreted as "mm" units. Note that the heatmap total height is determined by the number of cells, and the total row gaps defined by the number of row gaps with row_split multiplied by row_gap.
legend_height	grid::unit, default 6 cm (60 mm), to define the absolute height of the color gradient in the color key. This value is only used when heatmap_legend_param is not defined.
legend_cex	numeric default 1, used to scale the legend fontsize relative to the default fontsize 10. This value is only used when heatmap_legend_param is not defined.
top_annotation	HeatmapAnnotation as produced by ComplexHeatmap::HeatmapAnnotation() or NULL, used to display customized annotation at the top of the heatmap. The order of columns must match the order of columns in the data displayed in the heatmap.
outline	logical default TRUE, whether to draw an outline for each heatmap cell. Note: The outline is not drawn for style="dotplot" which already adds lines through the middle of each cell, not the border of each cell.
show_enrich	numeric default NULL, indicating which of the enrichment metrics to show as a label in each cell. When only one type is shown, there is no prefix, but for multiple types, a prefix is shown for each. The metrics in order include: "-log10P" "z-score" "number of genes"
use_raster	logical passed to ComplexHeatmap::Heatmap() indicating whether to rasterize the heatmap output, used when style="heatmap". Rasterization is not relevant to dotplot output since dotplot is drawn using an individual circle in each heatmap cell.
do_plot	logical indicating whether to display the plot with ComplexHeatmap::draw() or jamba::imageByColors() as relevant. The underlying data is returned invisibly.
...	additional arguments are passed to ComplexHeatmap::Heatmap() for customization.

Details

Note: It is recommended to call mem_plot_folio() with do_which=1 in order to utilize the gene-pathway content during clustering, which is more effective at clustering similar pathways by gene content. Otherwise pathways are clustered using only the -log10(p) enrichment P-value.

This function is a lightweight wrapper to ComplexHeatmap::Heatmap() intended to visualize the enrichment P-values from multiple enrichment results. The P-value threshold is used to colorize every cell whose P-value meets the threshold, while all other cells are therefore white.

Drawing Dotplot with Point Legend

The style argument controls whether a heatmap or dotplot is created.

• style="dotplot": each heatmap cell is not filled, and the color is drawn as a circle with size proportional to the number of genes involved in enrichment. A separate point legend is returned as an attribute of the heatmap object.

• style="dotplot_inverted": each heatmap cell is filled, and a circle is drawn with size proportional to the number of genes involved in enrichment. A separate point legend is returned as an attribute of the heatmap object.

To draw the dotplot heatmap including the point legend, use this command:

ComplexHeatmap::draw(hm,
   annotation_legend_list=attr(hm, "annotation_legend_list"))

Generally, the clustering using the gene-pathway incidence matrix is more effective at representing biologically-driven pathway clusters.

See Also

Other jam plot functions: adjust_polygon_border(), grid_with_title(), jam_igraph(), mem_gene_path_heatmap(), mem_legend(), mem_multienrichplot(), mem_plot_folio(), plot_layout_scale()

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.