Description Usage Arguments Details Value Author(s) Examples

View source: R/fmri_2dvisual.R

a visualization method, using `ggplot2`

to draw the brain
from axial, sagittal and coronal view with activated area identified by p-values

1 2 3 4 5 6 7 8 9 10 11 12 | ```
fmri_2dvisual(
pval,
axis_ls,
hemody_data = NULL,
mask,
p_threshold = 0.05,
legend_show = TRUE,
method = "scale_p",
color_pal = "YlOrRd",
multi_pranges = TRUE,
mask_width = 1.5
)
``` |

`pval` |
a 3D array of p-values used to plot activated area of the brain |

`axis_ls` |
a list with two elements. The first element is the character of 'x', 'y', 'z'. The second element is an integer showing a specific slice on the fixed axis identified in the first element. |

`hemody_data` |
a parameter to have the plot with/without hemodynamic contour. The default is NULL to make the plot without hemodynamic contour, otherwise assign a 3D array of the hemodynamic data. |

`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. |

`legend_show` |
a logical parameter to specify whether the final plot has legend |

`method` |
a string that represents method for the plot. There are 3 options: 'min_max', 'scale_p' and 'low5_percent'. The default is 'scale_p'. 'min_max' is to draw plot based on the color scale of the minimum and maximum of the p value; '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. |

`mask_width` |
a numeric value to specify the width of mask contour. The default is 1.5. |

The function `fmri_2dvisual`

is used to find activated part of the brain
based on given p values from sagittal, axial and coronal view. When providing input of
the p-values, the specific plane and index to slice on, the mask data and
the hemodynamic data of the brain, a plot will be generated with the heat map
for the activated parts, the black contour showing the position of the brain,
and the blue contour representing the hemodynamic contour.

a plot drawn by `ggplot2`

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

1 2 3 4 5 6 7 8 | ```
# sample 3D data of mask provided by the package
dim(mask)
# sample 3D p value provided by the package
dim(phase2_pval)
# plot the sagittal, coronal and axial view of this p value generated from the brain fMRI data
fmri_2dvisual(phase2_pval, list('x',40), hemody_data=NULL, mask=mask, p_threshold=0.05)
``` |

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