TCIU (version 1.2.7)

fmri_pval_comparison_3d: comparison between 3d visualization for p-values

Description

a visualization method, use plotly to compare the activated parts inside the brain, using two sets of color palettes. The activated parts are localized with different p values.

Usage

fmri_pval_comparison_3d(
  pval_3d_ls,
  mask,
  p_threshold,
  method_ls,
  color_pal_ls = list("YlOrRd", "YlGnBu"),
  multi_pranges = TRUE
)

Value

a plot drawn by plotly

Arguments

pval_3d_ls

a list of two element, each element is a 3D array of p-values used to plot activated area of the brain

mask

a 3D nifti or 3D array of data to show the shell of the brain

p_threshold

NULL or a numeric value that can be selected randomly below 0.05 to drop insignificant p-values of no need or drop no p-values. If 'low5_percent' method is used, make 'p_threshold' as NULL. The default is 0.05.

method_ls

a string that represents method for the plot. There are 2 options: 'scale_p' and 'low5_percent'. The default is 'scale_p'. 'scale_p' is to draw the plot with fixed color scale for fixed range of p value; 'low5_percent' is to draw the plot for the smallest 5 percent of p value when all the p values are not significant

color_pal_ls

a list of two element. Each element is the name of the color palettes provided by RColorBrewer. The default is list('YlOrRd', 'YlGnBu').

multi_pranges

an option under 'scale_p' method to decide whether there are at most 9 colors in the legend for the ranges of p value, or at most 4 colors. The default is TRUE, choosing the larger number of colors for the plot.

Author

SOCR team <http://socr.umich.edu/people/>

Details

The function fmri_pval_comparison_3d is used to visualize and compare the 3D plots of the activated parts in one brain shell. The activated parts are plotted based on p-values provided. Note that this comparison can only be made when the masks of the two p values are the same. When providing input of two set of the 3D array of p-values, corresponding p threshold for each p value data, and the method to draw the plot, the plot will be generated with one brain shell and two groups of activated parts in two sets of color palettes. The size and color of the scatter points represent different stimulated levels of the activated parts.

Examples

# sample 3D data of mask provided by the package
dim(mask)
# sample 3D p value provided by the package
dim(phase2_pval)
dim(phase3_pval)

fmri_pval_comparison_3d(list(phase2_pval, phase3_pval), mask, 
                        list(0.05, 0.05), list('scale_p', 'scale_p'), multi_pranges=FALSE)