plot_overlay: superimpose genesets onto plots

In lagelab/Genoppi: genoppi

superimpose genesets onto plots

Description

Takes a ggplot2 object and superimoses genes from a reference data.frame. This data.frame can be constructed manually or generated with a variety of functions, e.g. get_inweb_list, get_irefindex_list or get_tissue_list.

The function uses the mapping and plot environment from a previous ggplot to add an overlay with a matching 'reference' data.frame. This yields a new plot with items that intersect the the original ggplot data and the reference data. Can be applied iteratively. The user can input certain columns in the reference to gain more control over the plotting parameters of individual points. See notes for additional details.

Usage

plot_overlay(
  p,
  reference,
  match = "gene",
  size_gg = 3.5,
  stroke = 0.75,
  sig_text = NULL,
  insig_text = NULL,
  label = NULL,
  label_size = NULL,
  label_color = "black",
  col_significant = NULL,
  col_other = NULL,
  label_box_padding = 0.3,
  label_point_padding = 0.5,
  label_arrowhead_size = 0.01,
  label_max_overlaps = 10,
  legend_nchar_max = NULL,
  nchar_max_collapse = "<br>"
)

Arguments

p	A ggplot object passed down from plot_volcano_basic or plot_scatter_basic.
reference	a named list of data.frames.
match	string. By what string should the ggplot and overlay be merged? Default is 'gene'.
size_gg	numeric. Size of ggplot points.
stroke	numeric. The width of the outline/borders.
sig_text	string. Text for significant interactors to be displayed in legend.
insig_text	string. Text for non-significant interactors to be displayed in legend.
label	boolean. This will overwrite the label column in the reference data.frame.
label_size	numeric. Size of label. This will overwrite the label.size column in the reference data.frame.
label_color	string. The color of the label. Default is black.
col_significant	string. Color of superimposed genes that are significant.
col_other	string. Color of superimposed genes that are non-significant.
label_box_padding	numeric. Amount of padding around bounding box. See ?ggrepel::geom_text_repel.
label_point_padding	numeric. Amount of padding around label. See ?ggrepel::geom_text_repel.
label_arrowhead_size	numeric. The size of the arrowhead. 0 means no arrowhead.
label_max_overlaps	integer. Exclude text labels that overlap too many things. See ?ggrepel::geom_text_repel.
legend_nchar_max	integer. Maximum amount of allowed characters in the legend.
nchar_max_collapse	string. What character should be used for line break? Default is HTML line break "<br>".

Note

The following data.frame headers for a reference are accepted:

• "gene" A string tht indicates the gene name.

• "label" A boolen that indicates whether the label should be plotted.

• "label.size"A numeric that indicates the size of the label items.

See ?validate_reference for additional details.

Examples

## Not run: 
df <- example_data %>%
  calc_mod_ttest() %>%
  id_significant_proteins()

# overlay simple  a bait
df %>% 
  plot_volcano_basic() %>%
  plot_overlay(as.bait('BCL2')) 

# make a custom overlay with custom colors
myoverlay = data.frame(gene = c('FUS', 'RBMX'),
                       col_significant = c('cyan', 'blue'),
                       col_other = c('grey', 'grey'), 
                       dataset = c('group 1', 'group 2'))

# plot overlay
df %>% 
  plot_volcano_basic() %>%
  plot_overlay(list(overlay = myoverlay)) 

# plot multiple overlays
df %>% 
  plot_volcano_basic() %>%
  plot_overlay(list(overlay = myoverlay)) %>%
  plot_overlay(as.bait('BCL2')) 

## End(Not run)

lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.