mem_enrichment_heatmap | R Documentation |
MultiEnrichment Heatmap of enrichment P-values
mem_enrichment_heatmap(
mem,
style = c("dotplot", "heatmap"),
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,
cluster_rows = TRUE,
column_fontsize = NULL,
column_cex = 1,
cluster_columns = FALSE,
sets = NULL,
color_by_column = FALSE,
cex.axis = 1,
lens = 3,
cexCellnote = 0,
column_title = NULL,
row_names_max_width = grid::unit(30, "cm"),
column_names_max_height = grid::unit(30, "cm"),
heatmap_legend_param = NULL,
legend_height = grid::unit(6, "cm"),
legend_cex = 1,
apply_direction = FALSE,
direction_cutoff = 0,
gene_count_max = NULL,
top_annotation = NULL,
show = NULL,
use_raster = FALSE,
do_plot = TRUE,
...
)
mem |
|
style |
|
p_cutoff |
|
min_count |
|
p_floor |
|
point_size_factor |
|
point_size_min, point_size_max |
|
row_method |
|
name |
|
row_dend_reorder |
|
row_fontsize, column_fontsize |
optional |
cluster_columns |
|
sets |
|
color_by_column |
|
cex.axis |
|
lens |
|
cexCellnote |
|
column_title |
optional |
row_names_max_width, column_names_max_height, heatmap_legend_param |
arguments passed to |
top_annotation |
|
use_raster |
|
do_plot |
|
... |
additional arguments are passed to |
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.
The style
argument controls whether a heatmap or dotplot is
created. When style="dotplot"
the cells are colored as usual
but are drawn as circles sized proportional to the number of
genes involved in enrichment. Because ComplexHeatmap::Heatmap()
is used for this step, a separate point legend is returned
as an attribute of the heatmap object.
To draw the dotplot heatmap including the point legend, use this form:
ComplexHeatmap::draw(hm, annotation_legend_list=attr(hm, "annotation_legend_list"))
Note that this function may be more easily applied through the
wrapper function with the format mem_plot_folio(mem, do_which=1, ...)
.
The wrapper function mem_plot_folio()
performs hierarchical
clustering of the underlying gene-pathway incidence matrix, which
informs the clustering of enrichment results shown
in this function mem_enrichment_heatmap()
. Otherwise, this
function will cluster pathways using only the enrichment
P-values transformed with -log10(p)
. Generally, the clustering
using the gene-pathway incidence matrix is more effective at
representing biologically-driven pathway clusters.
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()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.