pval_plot

Internal function to convert an object of class 'im' to values readable by <code>image.plot</code> function within the <code>rrs</code>, <code>lotrrs</code>, and <code>gating</code> functions.

internal

Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.

Ian D. Buller

gateR

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Elena Hsieh

Debashis Ghosh

Lance A. Waller

NCI 

pval_plot function

<dl><dt>input</dt>
<dd>An object of class 'rrs' from the <code>rrs</code> or <code>lotrrs</code> function.</dd>
<dt>alpha</dt>
<dd>Numeric. The two-tailed alpha level for significance threshold (default in <code>rrs</code>, <code>lotrrs</code>, and <code>gating</code> functions is 0.05).</dd></dl>

Arguments

Prepare significant p-values for plotting — pval_plot

<dl>

<dt>input</dt>
<dd>An object of class 'rrs' from the <code>rrs</code> or <code>lotrrs</code> function.</dd>


<dt>alpha</dt>
<dd>Numeric. The two-tailed alpha level for significance threshold (default in <code>rrs</code>, <code>lotrrs</code>, and <code>gating</code> functions is 0.05).</dd>

</dl>

pval_plot: Prepare significant p-values for plotting

Description

Usage

Value

Arguments