plot_IQR_condition_exp: Get and plot the IQRs of submatrices of the correlation...
In hansenlab/spqn: Spatial quantile normalization

Description Usage Arguments Value Note Examples

View source: R/functions_evaluation.R

The get_IQR_condition_exp function computes the IQRs of a set of 10 by 10 same-size bins that partition the correlation matrix, ordered according to expression level.

The plot_IQR_condition_exp function plots the IQR for each bin among a set of 10 by 10 same-size bins that partition the correlation matrix, with IQR denoted by the width of boxes in the plot.

1 2	get_IQR_condition_exp(cor_mat, ave_exp) plot_IQR_condition_exp(IQR_list)

`cor_mat`	correlation matrix, generated by gene expression matrix, with genes sorted by average expression levels.
`ave_exp`	vector, average expression level of each gene for the normalized gene expression matrix.
`IQR_list`	List, output of `get_IQR_condition_exp`.

A plot with boxes that shows the IQR of each bin

The mnemonic for condition_exp is ‘conditional on expression’.

if(require(spqnData)) {
    data(gtex.4k)
    cor_mat <- cor(t(assay(gtex.4k)))
    ave_logrpkm <- rowData(gtex.4k)$ave_logrpkm
    IQR_list <- get_IQR_condition_exp(cor_mat, ave_exp = ave_logrpkm)
    plot_IQR_condition_exp(IQR_list)
    }