extractGaps: Extract the Positions of Spacing from Clustered Groups

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

Extract the Positions of Spacing from Clustered Groups

Description

Very similar to extractClusters but for the gaps that appear between the clusters when row.groups or col.groups are set in the heatmap functions. Useful in conjunction with ExtractMatrix if spaces between the groups want to be maintained or widened without actually clustering the data. Output can be supplied to gaps.row and gaps.col in myHeatmap or gaps.row.spec and gaps.col.spec in myHeatmapByAnnotation

Usage

extractGaps(data, heatmap, extractRows = FALSE, extractCols = TRUE,
  num_Rows = 5, num_Cols = 5)

Arguments

data	numeric data matrix with samples/observations in the columns and genes/variables in the rows. Should be the same data supplied to the heatmap function
heatmap	Output of a heatmap generated from myHeatmap or myHeatmapByAnnotation. The heatmap generated from these functions can be saved to a variable which should serve as the input here. IMPORTANT. The heatmap supplied here MUST have show.colnames and show.rownames = TRUE.
extractRows	logical. should gaps along clustered rows be extracted. At least one of extractRows and extractCols must be set to TRUE
extractCols	logical. should gaps along clustered columns be extracted. At least one of extractRows and extractCols must be set to TRUE
num_Rows	number of clusters along the rows for which the gaps should be extract. Default set to 5.
num_Cols	number of clusters along the columns for which the gaps should be extract. Default set to 5.

Value

a numericvector or a list object of two numeric vectors (in a case where both rows and columns are extracted) where the positions of each gap along the rows/columns is indicated.

Note

a similar output can be obtained from using extractClusters where gaps would equal the cumulative sum of the frequency of each cluster from the output (cumsum(table(output)))

Author(s)

~~Alison Moss~~

See Also

See also extractClusters, ExtractMatrix

Examples

##initate parameters
initiate_params()

##view heatmap with clusters separated
heatmap <- myHeatmap(RAGP_norm, row.groups = 7, col.groups = 6, show.colnames = TRUE)

##extract gaps for numeric vector of where gaps should be
gaps <- extractGaps(RAGP_norm, heatmap = heatmap, extractRows = TRUE, extractCols = TRUE,
  num_Rows = 7, num_Cols = 6)

##extract matrix, use matrix and gaps to plot heatmap with expanded space between gaps
mat <- ExtractMatrix(RAGP_norm, heatmap = heatmap)
myHeatmap(mat, clust.cols = FALSE, clust.rows = FALSE, gaps.row = gaps$Row_Groups,
  gaps.col = gaps$Col_Groups)
myHeatmap(mat, clust.cols = FALSE, clust.rows = FALSE, gaps.row = gaps$Row_Groups,
  gaps.col = gaps$Col_Groups, gap.width = 3)  ##expands all gaps by gap.width

myHeatmap(mat, clust.cols = FALSE, clust.rows = FALSE, gaps.row = sort(rep(gaps$Row_Groups,6)),
  gaps.col = sort(rep(gaps$Col_Groups,2)))  ##expands row gaps by 6 and column gaps by 2

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.