Description Usage Arguments Details Value Author(s) Examples

View source: R/fmri_3dvisual.R

a visualization method, using `plotly`

to draw the 3D plot of the brain
with the activated areas determined by p-values, which is generated from fMRI data

1 2 3 4 5 6 7 8 9 | ```
fmri_3dvisual(
pval,
mask,
p_threshold = 0.05,
method = "scale_p",
color_pal = "YlOrRd",
multi_pranges = TRUE,
title = NULL
)
``` |

`pval` |
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 all p-values above the threshold. If 'low5_percent' method is used, make 'p_threshold' as NULL. The default is 0.05. |

`method` |
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` |
the name of the color palettes provided by |

`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. |

`title` |
the title of the plot. The default is NULL. |

The function `fmri_3dvisual`

is used to visualize the 3D plot of the brain
with its activated parts based on provided p values. The p values are generated by
applying statistical test on fMRI data. When providing input of a 3D p-values data,
a 3D interactive plot will be generated with surface for the brain shell
and scatter points in different colors and size representing different stimulated levels.

a list of two elements

plot - the 3d plot of the fMRI data drawn by

`plotly`

pval_df - data.frame with the p value for each voxel and the specified color for it

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

1 2 3 4 5 6 7 | ```
# sample 3D data of mask provided by the package
dim(mask)
# sample 3D p value provided by the package
dim(phase2_pval)
# make the 3D plot
fmri_3dvisual(phase2_pval, mask, p_threshold = 0.05, method="scale_p")$plot
``` |

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