# Introduction¶

PRSice will automatically generate the bar-plot and high-resolution plot (if --fastscore) is not set. Quantile plots will also be generated if you used the --quantile parameter.

To see some example of PRSice output, you can refer to here

Note

These parameters, is not recognized by the PRSice binary

# Command¶

• --bar-col-high

Colour of the most predicting threshold. Default: firebrick

• --bar-col-lower

Colour of the poorest predicting threshold. Default: dodgerblue

• --bar-col-p

When set, will change the colour of bar to p-value threshold instead of the p-value from the association with phenotype

• --bar-palatte

Colour palatte to be used for bar plotting when --bar_col_p is set. Default: YlOrRd

• --multi-plot

Plot the top N target phenotypes / gene sets in a summary plot

• --plot

When set, will only perform plotting using existing PRSice result files. Users will still need to provide all other parameters such that PRSice can correctly locate the required input files for plotting.

• --plot-set

The default behaviour of PRSet is to plot the bar-chart, high-resolution plot and quantile plot of the "Base" gene set, which consider all SNPs within the genome. By using the --plot-set option, you can plot the specific set of interest.

• --quantile | -q

Number of quantiles to plot. No quantile plot will be generated when this is not provided.

• --quant-extract | -e

File containing sample ID to be plot on a separated quantile e.g. extra quantile containing only schizophrenia samples. Must contain IID. Should contain FID if --ignore-fid isn't set.

!!! note

This will only work if the base and target has a different
phenotype or if the target phenotype is quantitative

• --quant-ref

Reference quantile for quantile plot. Default is number of quantiles divided by 2

• --scatter-r2

When set, will change the y-axis of the high resolution scatter plot to R2 instead