NormalizeColor

Helper for computing colors for embedding plots

Provides a smooth mapping of multidimensional points into
low-dimensional space defined by a self-organizing map. Designed to work
with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019)
<doi:10.12688/f1000research.21642.1>.

Mirek Kratochvil

EmbedSOM

Fast Embedding Guided by Self-Organizing Map

Sofie Van Gassen

Britt Callebaut

Yvan Saeys

Ron Wehrens

NormalizeColor function

<dl><dt>data</dt>
<dd>Vector of scalar values to normalize between 0 and 1</dd>
<dt>low, high</dt>
<dd>Originally quantiles for clamping the color.
Only kept for backwards compatibility, now ignored.</dd>
<dt>pow</dt>
<dd>The scaled data are transformed to data^(2^pow). If set to 0,
nothing happens. Positive values highlight differences in the
data closer to 1, negative values highlight differences closer to 0.</dd>
<dt>sds</dt>
<dd>Inverse scale factor for measured standard deviation
(greater value makes data look more extreme)</dd></dl>

Arguments

Helper for computing colors for embedding plots — NormalizeColor

<dl>

<dt>data</dt>
<dd>Vector of scalar values to normalize between 0 and 1</dd>


<dt>low, high</dt>
<dd>Originally quantiles for clamping the color.
Only kept for backwards compatibility, now ignored.</dd>


<dt>pow</dt>
<dd>The scaled data are transformed to data^(2^pow). If set to 0,
nothing happens. Positive values highlight differences in the
data closer to 1, negative values highlight differences closer to 0.</dd>


<dt>sds</dt>
<dd>Inverse scale factor for measured standard deviation
(greater value makes data look more extreme)</dd>

</dl>

NormalizeColor: Helper for computing colors for embedding plots

Description

Usage

Arguments

Examples