mouse_subregions_plot: mouse_subreginos_plot

Description Usage Arguments Value Examples

View source: R/mouseplot.R

Description

Plot gene expression values for strucutures at a given ontology depth for the mouse or developing mouse atlas. This function pull the mean expression energies directly from the Allen institute API. Utilizes WGCNA's verboseBarplot function for visualization.

Usage

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mouse_subregions_plot(
  gene,
  atlas,
  log_transform = FALSE,
  experiment = NULL,
  struct_depth = 3,
  im_width = NULL,
  im_height = NULL,
  save_pdf = TRUE
)

Arguments

gene

Gene in the Allen Mouse or Developing Mouse atlas; character string

atlas

Atlas to plot the gene for; either "DevMouse" or "Mouse"

log_transform

Boolean for log vs linear data

experiment

Experiment ID string; Experiment ID for the adult mouse atlas. The devmouse uses all experiments, so the ID is ignored. If not ID is provided, the program will ask you to choose one from a list.

struct_depth

ontology structure depth; default of 3. It is often useful creating multiple plots with different structure depths for comparison.

im_width

Output image width; optional. Note that if the plot is too narrow, not all brain structure names will show up.

im_height

Output image height; optional

save_pdf

Save plot to disk as pdf or return to console

Value

Creates a new plot of the gene in the current working directory

Examples

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# call on a given gene
mouse_structureplot("Scarf1", atlas="Mouse")

# call a given gene with a specific experiment
mouse_structureplot("Shh", atlas="DevMouse", struct_depth = 4, im_width = 25)

AllenInstitute/atlasplot documentation built on Aug. 11, 2021, 1:52 a.m.