Advanced: Analysis Display Parameters

Nearly all of the analyses performed by 𝑓(Cell) produce graphical plots or images of the results. In this section, we will go through the different outputs available in this version of 𝑓(Cell), as well as how to modify their appearance.

Displaying the data created by 𝑓(Cell)

There are numerous possible outputs:

1. A "population-based" summary of the iORGs, where all summaries are displayed overlapping on a single plot.
2. A "population-based" summary of the iORGs, where all summaries are displayed according to their order of acquisition (so for 10 acquisitions in 3 trials, it would display 10 plots, with 3 summaries in each).
3. "Individual-cell" summaries of the iORGs, where all acquisitions for each query location are combined, then displayed in aggregate (e.g. a histogram).
4. "Individual-cell" summaries of the iORGs, where all acquisitions for each query location are combined, then displayed overlapping on a single plot.

Each of the JSON objects corresponding to these outputs can be seen below:

Key	Parent Key	Type	Options	Description
"pop_summary_overlap"	"display_params"	JSON Object	none	A JSON object holding parameters for to the "population-based" summary of the iORGs.
"pop_summary_seq"	"display_params"	JSON Object	none	A JSON object holding parameters for "population-based" summary of the iORGs, but plotted "end-to-end"
"indiv_summary"	"display_params"	JSON Object	none	A JSON object holding parameters for individual-cell" summaries of the iORGs.
"indiv_summary_overlap"	"display_params"	JSON Object	none	A JSON object holding parameters for individual-cell" summaries of the iORGs, plotted overlapping each other.

Population-based summary of ORGs:

The population-based summary of ORGs was one of the first methods of summarizing ORG data, and presented in Cooper et. al. 2017. We provide numerous ways of visualizing these signals, depending on your specific needs. Examples of each are shown below.

Displaying all population-based summaries on the same plot:

Key	Parent Key	Type	Options	Description
"stimulus"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display population-summarized ORG data that was obtained during a stimulus, but WASN'T made relative to the control data. Shown here.
"control"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display population-summarized ORG data that was obtained without delivering a stimulus. Shown here.
"relative"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display population-summarized ORG data that was obtained during a stimulus, but WAS made relative to the control data, via any of the methods described in the ORG summary section. Shown here.
"pooled"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display the pooled population-summarized ORG data, where the average +- 1 confidence is displayed. Shown here.
"cross_group"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display the pooled population-summarized ORG data on a separate plot, across groups. (Example: plotting ORG summaries from multiple eccentricities on the same plot)
"annotations"	"pop_summary_overlap"	boolean	(**false**, true)	Whether or not to display metric annotations on the pooled population-summarized ORG data.
"axes"	"pop_summary_overlap"	JSON Object	none	A JSON object holding parameters that control the appearance of the plots in this JSON object.

  "pop_summary_seq": {
    "stimulus": false,
    "relative": false,
    "num_in_seq": 14,

Displaying all population-based summaries on the same plot:

Key	Parent Key	Type	Options	Description
"stimulus"	"pop_summary_seq"	boolean	(**false**, true)	Whether or not to display population-summarized ORG data in a sequence of plots that was obtained during a stimulus, but WASN'T made relative to the control data.
"relative"	"pop_summary_seq"	boolean	(**false**, true)	Whether or not to display population-summarized ORG data in a sequence of plots that was obtained during a stimulus, but WAS made relative to the control data, via any of the methods described in the ORG summary section.
"num_in_seq"	"pop_summary_seq"	int	**null**	The number of acquisitions in a single trial. The software will place a population summary in a given plot by calculating the modulus of this value and the difference between the lowest VidNum of the stimulus datasets, and the current dataset.
"axes"	"pop_summary_seq"	JSON Object	none	A JSON object holding parameters that control the appearance of the plots in this JSON object.

Examples:

Stimulus-only, control-only, and relativized population ORG summaries:

Pooled ORG summaries (shading is +- 1 CI):

Population-based summary of ORGs:

Axes objects

Each of the above outputs can have its plot appearances extensively customized.

Key	Parent Key	Type	Options	Description
"xmin"	"axes"	float	**null**	The minimum X-axis value displayed on the plot/image. If null, then the X-axis minimum is determined according to the rules defined by Matplotlib.
"xmax"	"axes"	float	**null**	The maximum X-axis value displayed on the plot/image. If null, then the X-axis maximum is determined according to the rules defined by Matplotlib.
"ymin"	"axes"	float	**null**	The minimum Y-axis value displayed on the plot/image. If null, then the Y-axis minimum is determined according to the rules defined by Matplotlib.
"ymax"	"axes"	float	**null**	The maximum Y-axis value displayed on the plot/image. If null, then the Y-axis maximum is determined according to the rules defined by Matplotlib.
"cmap"	"axes"	"string"	(**"plasma"**, any)	Any colormap string (recognized by Matplotlib)[https://matplotlib.org/stable/gallery/color/named_colors.html].
"legend"	"axes"	boolean	(**false**, true)	Whether or not to display the plot's legend.