mouse_subregions_plot: mouse_subreginos_plot

In AllenInstitute/atlasplot: Easy Plotting of the Allen Brain Altases

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

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

# 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.