plotNhoodMA: Visualize DA results as an MAplot

plotNhoodMAR Documentation

Visualize DA results as an MAplot

Description

Visualize DA results as an MAplot

Usage

plotNhoodMA(da.res, alpha = 0.05, null.mean = 0)

Arguments

da.res

A data.frame of DA testing results

alpha

A numeric scalar that represents the Spatial FDR threshold for statistical significance.

null.mean

A numeric scalar determining the expected value of the log fold change under the null hypothesis. default=0.

Details

MA plots provide a useful means to evaluate the distribution of log fold changes after differential abundance testing. In particular, they can be used to diagnose global shifts that occur in the presence of confounding between the number of cells acquired and the experimental variable of interest. The expected null value for the log FC distribution (grey dashed line), along with the mean observed log fold change for non-DA neighbourhoods (purple dashed line) are plotted for reference. The deviation between these two lines can give an indication of biases in the results, such as in the presence of a single strong region of DA leading to an increase in false positive DA neighbourhoods in the opposite direction.

Value

a ggplot object

Author(s)

Mike Morgan

Examples

NULL


MikeDMorgan/miloR documentation built on Aug. 7, 2022, 8:21 a.m.