plotConnectivity: Plot a connectivity matrix
In jayaraman-lab/neuprintrExtra: Extra functions to analyze neuprint EM datasets

Description Usage Arguments Details Value

Plot a connectivity matrix

plotConnectivity(
  connObj,
  slctROI = NULL,
  grouping = "type",
  connectionMeasure = "weightRelative",
  xaxis = c("inputs", "outputs"),
  facetInputs = NULL,
  facetOutputs = NULL,
  theme = theme_minimal(),
  cmax = NULL,
  replacementLabels = NULL,
  orderIn = NULL,
  orderOut = NULL,
  legendName = NULL,
  showTable = "inputs",
  switch = NULL,
  flipy = FALSE,
  flipy_facet = FALSE
)

`connObj`	A connectivity object. Either a connectivity table, a matrix with `dimnames` Inputs and Outputs(as returned by `connectivityMatrix`) or a `connectivityCluster` object.
`slctROI`	For connectivity tables, you can specify a ROI
`grouping`	Which variable to use. Will be ignored when `connObj` is a `connectivityCluster` (the decision has already been made while clustering). Any variable postfixed by "to" or "from" in the table is a valid value, as well as "bodyid" and "neuron"
`connectionMeasure`	Which variable to use as a plotting value
`xaxis`	Should inputs or outputs be on the x axis (will match the value to "inputs" or "outputs")
`facetInputs`	Variable to facet the inputs on (nothing by default)
`facetOutputs`	Variable to facet the outputs on (nothing by default)
`theme`	A theme to use
`cmax`	Maximum fill value for the color scale. By default the maximum value found in the table.
`replacementLabels`	A column prefix to use as a replacement for the axis labels (useful to replace bodyids with names for example)
`orderIn`	A vector of input bodyid/types/names in the desired order, or a connectivityCluster object. Optional ordering of the inputs (ignored and replaced by the clustering order if connObj is a connectivityCluster).
`orderOut`	A vector of output bodyid/types/names in the desired order, or a connectivityCluster object. Optional ordering of the outputs (ignored and replaced by the clustering order if connObj is a connectivityCluster).
`legendName`	Optional override the default name for the color legend (by default a prettification of connectionMeasure)
`showTable`	When both inputs and outputs have been used for a clustering (via `clusterBag`), which connectivity table to show.
`switch`	To be passed to `ggplot2::facet_grid` to switch where the facet labels are displayed.
`flipy`	Option to flip the y axis order
`flipy_facets`	Option to flip the y axis facets order