plotRTgroup: Helper to visualize feature grouping
In HimesGroup/qmtools: Quantitative Metabolomics Data Processing Tools

plotRTgroup

R Documentation

Helper to visualize feature grouping

Description

Visualizes feature grouping results produced by clusterFeatures. A retention-time based feature group is displayed with its sub-groups based on the feature intensity correlations either using a pair plot or graph. Features with the same color indicate that they are in the same group.

Usage

plotRTgroup(
  x,
  i,
  group,
  type = c("graph", "pairs"),
  rtime_group_var = "rtime_group",
  feature_group_var = "feature_group",
  cor_cut = 0.7,
  cor_use = c("everything", "all.obs", "complete.obs", "na.or.complete",
    "pairwise.complete.obs"),
  cor_method = c("pearson", "kendall", "spearman"),
  log2 = FALSE
)

Arguments

`x`	A SummarizedExperiment object.
`i`	A string or integer value specifying which assay values to use. Choose the same value used in the feature grouping.
`group`	A string specifying the label of retention time-based group to visualize.
`type`	A string specifying which type of plots to visualize.
`rtime_group_var`	A string specifying the names of variable containing the retention-time based grouping result in `rowData(x)`.
`feature_group_var`	A string specifying the names of variable containing the final feature grouping result in `rowData(x)`.
`cor_cut`	A numeric value specifying a cut-off for the visualizing correlations in a graph as edges. Ignored if type is "pairs".
`cor_use`	A string specifying which method to compute correlations in the presence of missing values. Refer to `?cor` for details. Choose the same value used in the feature grouping. Ignored if type is "pairs".
`cor_method`	A string specifying which correlation coefficient is to be computed. See `?cor` for details. Choose the same value used in the feature grouping. Ignored if type is "pairs".
`log2`	A logical specifying whether feature intensities needs to be log2-transformed before calculating a correlation matrix. Ignored if type is "pairs". Choose the same value used in the feature grouping.

Value

A graph or pair plot.

Examples


data(faahko_se)

## Clustering
se <- clusterFeatures(faahko_se, i = "knn_vsn", rtime_var = "rtmed")

## Graph
plotRTgroup(se, i = "knn_vsn", group = "FG.22")

## Pairwise scatter
plotRTgroup(se, i = 3, group = "FG.22", cor_method = "spearman",
            log2 = TRUE, type = "pairs")

HimesGroup/qmtools documentation built on April 16, 2023, 8 p.m.