autoplot: Automatic Parameters Detection for IFC Graphs
In IFC: Tools for Imaging Flow Cytometry

autoplot

R Documentation

Automatic Parameters Detection for IFC Graphs

Description

Function intended to generate IFC graphs with minimal inputs from users.
It is essentially based on automatic detection of graphical parameters thanks to 'shown_pops' argument.

Usage

autoplot(
  obj,
  shown_pops = NULL,
  subset = NULL,
  x = NULL,
  x_trans = NULL,
  y = NULL,
  y_trans = NULL,
  type = NULL,
  smoothingfactor = NULL,
  normalize = NULL,
  bin,
  viewport = "ideas",
  precision = c("light", "full")[1],
  color_mode = c("white", "black")[1],
  draw = TRUE,
  ...
)

Arguments

`obj`	an 'IFC_data' object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).
`shown_pops`	one or several populations present in 'obj'. Default is NULL. If provided, `autoplot` will try to display these populations. See details when not provided. `autoplot` will try to determine x and y and their transformations based on 'shown_pops' parameter. If all populations provided in 'shown_pops' are siblings, region(s) from which 'shown_pops' were defined will be displayed. In case 'shown_pops' are not siblings, they will be treated as populations and a graph will be generating with an overlay of these populations. Order of this overlay is given by order of 'shown_pops'. Finally, changing any of the following arguments (x, x_trans, y, y_trans, type) to something else than the one detected from 'shown_pops' will prevent from displaying region(s) and 'shown_pops' populations will be displayed as overlay. However, please consider that if original type is 'histogram' changing x_trans transformation will have no impact on this.
`subset`	a population present in 'obj'. Default is NULL. Background population that will be used to generate graph. This argument will not be used when graph is an histogram. If this argument is filled with a different population than what can be determined thanks to 'shown_pops', Then 'shown_pops' will be treated as overlay. However, 'shown_pops' argument can still be used to determine x, y axis and their transformation
`x`	feature for x-axis. Default is NULL. When empty, `autoplot` will try to determine if automatically from 'shown_pops' argument. If provided, x feature has to be a name from 'obj' features. Note that providing x feature : - takes precedence on automatic x-axis detection. - will reset x-axis transformation to "P" except if 'x_trans' is filled.
`x_trans`	parameter for x-axis transformation. Default is NULL. If not provided, transformation will be determined thanks to 'shown_pops'. It takes precedence when provided and if provided it has to be be either "P" or coercible to a positive numeric. "P" will leave x-axis as is but a positive numeric will be passed has hyper argument of `smoothLinLog` to transform x-axis.
`y`	feature for y-axis. Default is NULL. When empty, `autoplot` will try to determine it automatically from 'shown_pops' argument. If provided, y feature has to be a name from obj features. Note that providing y feature - takes precedence on automatic y-axis detection. - will reset y-axis transformation to "P" except if 'y_trans' is filled.
`y_trans`	parameter for y-axis transformation. Default is NULL. If not provided, transformation will be determined thanks to 'shown_pops'. It takes precedence when provided and and if provided it has to be be either "P" or coercible to a positive numeric. "P" will leave y-axis as is but a positive numeric will be passed has hyper argument of `smoothLinLog` to transform y-axis. Note that it is irrelevant for "histogram".
`type`	type of plot. Default is NULL to allow `autoplot` to detemine 'type' automatically. If provided it has to be either "histogram", "scatter", "density". Note that when "histogram" is choosen, 'subset' parameter will not be used. Note that "density" will be possible only when 'subset' will be automatically determined or filled with only one population. Note that when `autoplot` has determined, thanks to 'shown_pops' that original plot is an "histogram", "Object Number" will be used as y-axis by default when 'type' is forced to "scatter" or "density".
`smoothingfactor`	when type of graph is "histogram", whether to smooth it or not. Default is NULL. Should be an integer [0:20] Note that 0 means no smoothing and other values will produce smoothing
`normalize`	when type of graph is "histogram", whether to normalize it or not. Default is NULL. Should be a logical.
`bin`	number of bins when graph's type is "histogram" / number of equally spaced grid points for density. Default is missing to allow `autoplot` to determine it by itself.
`viewport`	Either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas". -"ideas" will use same limits as the one defined in ideas. -"data" will use data to define limits. -"max" will use data and regions drawn to define limits.
`precision`	when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light". -"light", the default, will only display points of same coordinates that are amoung the other layers. -"full" will display all the layers.
`color_mode`	Whether to extract colors from obj in white or black mode. Default is "white".
`draw`	whether to draw plot. Default is TRUE.
`...`	Other arguments to be passed.

Details

when 'shown_pops' are not provided, autoplot can't determine anything.
So, if not provided default values will be used:
-'subset' = "All"
-'x' = "Object Number"
-'x_trans' = "P"
-'y' = "Object Number"
-'y_trans' = "P"
-'type' = "histogram"