vizConnectogram

Visualizing brain connectivity profiles with multiple connectogram

vizConnectogram(
  data,
  hot = "#F8766D",
  cold = "#00BFC4",
  ncol = 1,
  nrow = 1,
  edgethickness = 0.8,
  filename = "conn.png",
  colorscheme,
  title,
  width = 1000,
  height = 1050,
  leg.height = 200,
  margins = c(1.2, 1.2, 1, 1.5),
  node.size,
  node.text.size = 1,
  legend.text.size = 7,
  legend.title.size = 8,
  limits,
  title.size = 11,
  title.alignment = "center",
  colorbar_title = "Edge Strength",
  edge_labels = c("Positive", "Negative"),
  row_title
)

Arguments

data

a matrix of edge values with 4005, 7021, 23871 or 30135 columns

hot

color for the positive connections. Set to #F8766D by default.

cold

color for the negative connections. Set to #00BFC4 by default.

ncol

number of columns in the plot. Not used for single row data

nrow

number of rows in the plot. Not used for single row data

edgethickness

a value to adjust the thickness of the edges. Set to 0.8 by default.

filename

output filename with a *.png file extension. Set to "conn.png" by default

colorscheme

an optional vector of color names or color codes to color code the networks.

title

a vector of strings to be used as title

width

width (in pixels) of each connectogram. Set to 1000 by default. Not used for single row data

height

height (in pixels) of each connectogram . Set to 1050 by default. Not used for single row data

leg.height

height (in pixels) of legend, in pixels. Set to 100 by default. Not used for single row data

margins

vector of 4 values specifying the amount of empty space on the left, right, top and bottom for each connectogram. Set to c(1.2,1.2,1,1.5) by default. You might want to adjust these values if the text labels get cut off by a neighbouring connectogram or the legend. Not used for single row data

node.size

size parameter for the dots representing the nodes. If not specified, an appropriate size will be set.

node.text.size

size parameter for the text labels on the nodes. Set to 1 by default.

legend.text.size

size parameter for the legend text. Set to 6 by default.

legend.title.size

size parameter for the legend title. Set to 8 by default.

limits

a pair of values that governs the limits of the edge strengths displayed. If missing limits=range(abs(data),na.rm=T)

title.size

size parameter for the title. Set to 11 by default.

title.alignment

string object specifying title's alignment relatively to its plot options are 'left', 'center' (default), 'right'.

colorbar_title

title for the colorbar legend

edge_labels

Vector of two strings defining the labels for the edge legends. Default is c("Positive","Negative").

row_title

a vector of strings to be used as left vertical titles for each row of plots when there are many

Value

outputs a .png image

Details

This function takes a matrix (NROW=number of edges in the connectome; NCOL=number of edges in the connectome) of edge values and visualizes the edge-to-edge connectivity with multiple connectograms

Examples

if (FALSE) {
data=matrix(sample(c(1,0, -1), 23871*6, replace = TRUE, prob = c(0.001, 0.998,0.001)),nrow=6)
vizConnectogram(data=data,ncol=3, nrow=2)
}