dotplot

The function is used to draw a graph to reflect the univariate HRs and P-values of the pathways in different cancer types.

A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.

Junwei Han

ssMutPA

Single-Sample Mutation-Based Pathway Analysis

Yalan He

Qian Wang

dotplot function

<dl><dt>data</dt>
<dd>A pathway activity score matrix, which rows represent the pathways and the columns are samples.</dd>
<dt>low_col, high_col</dt>
<dd>Colours for low and high ends of the gradient.</dd>
<dt>cut_point</dt>
<dd>The threshold of HRs,when HR is greater than the cut_point,HR is assigned cut_point.</dd></dl>

Arguments

Plotting the Dot plot. — dotplot

<dl>

<dt>data</dt>
<dd>A pathway activity score matrix, which rows represent the pathways and the columns are samples.</dd>


<dt>low_col, high_col</dt>
<dd>Colours for low and high ends of the gradient.</dd>


<dt>cut_point</dt>
<dd>The threshold of HRs,when HR is greater than the cut_point,HR is assigned cut_point.</dd>

</dl>

dotplot: Plotting the Dot plot.

Description

Usage

Value

Arguments

Examples