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.
There are numerous possible outputs:
- A "population-based" summary of the iORGs, where all summaries are displayed overlapping on a single plot.
- 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).
- "Individual-cell" summaries of the iORGs, where all acquisitions for each query location are combined, then displayed in aggregate (e.g. a histogram).
- "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. |
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.
| 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. An example can be found here. |
"control" |
"pop_summary_overlap" |
boolean |
(**false**, true) |
Whether or not to display population-summarized ORG data that was obtained without delivering a stimulus. An example can be found 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. An example can be found 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. An example can be found 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. Details can be found here. |
| 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. Details can be found here. |
The individual query locations were first presented in Cooper et. al. 2020. We provide numerous ways of visualizing these signals, depending on your specific needs. Examples of each are shown below.
| Key | Parent Key | Type | Options | Description |
|---|---|---|---|---|
"histogram" |
"indiv_summary" |
boolean |
(**false**, true) |
Whether or not to display histograms of all metrics extracted from individual-query-location summaries. Available metrics can be found here, and an example can be found here. |
"cumulative_histogram" |
"indiv_summary" |
boolean |
(**false**, true) |
Whether or not to display cumulative histograms of all metrics extracted from individual-query-location summaries. Available metrics can be found here, and an example can be found here. |
"map_overlay" |
"indiv_summary" |
int |
**null** |
Whether or not to display color-coded overlays of all metrics extracted from individual-query-location summaries. Available metrics can be found here, and an example can be found here. |
"axes" |
"indiv_summary" |
JSON Object |
none |
A JSON object holding parameters that control the appearance of the plots in this JSON object. Details can be found here. |
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. |
"xstep" |
"axes" |
float |
**null** |
The X-axis step used for histograms. Ignored otherwise. If null, then the steps are selected automatically based on the 1st and 99th percentile. |
"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. |