seekCluster: k-means clustering for rows and hierarchical clustering for...
In Solatar/seeqR:

Description Usage Arguments Value Examples

Imports: ggplot2, reshape2 tibble

seekCluster(
  data0,
  k = 2,
  scale = T,
  samplecluster = T,
  kmeans.resample = 50,
  maxrecenter = 10,
  dendro.distmethod = "euclidean",
  dendro.linkmethod = "complete",
  tileColors = c("royalblue4", "white", "red"),
  showRows = F,
  helpLinesV = NA,
  helpLinesH = FALSE,
  ownCluster = NA,
  showClusters = F,
  tileSepColor = NA
)

`data0`	data.frame, where rows are genes and columns are samples (possibility of having gene names as row names)
`k`	integer, setting the number of clusters to be used (determine with seekKmeansClusterNumber())
`samplecluster`	boolean, should clustering of samples be performed
`kmeans.resample`	integer, number of times the the algorithm repeats its procedure with random starting points
`maxrecenter`	integer, maximum number of times the algorithm re-centeres the cluster by mean and re-assigns the data points. This is done until the clusters do not change anymore but maximum as many times as specified here.
`dendro.distmethod`	string, one of: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski"
`dendro.linkmethod`	string, one of: "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid"
`tileColors`	vector of 3 strings depicting colors for low, medium & high values
`showRows`	boolean, should row names be displayed in heatmap?
`helpLinesV`	vector of numbers, indicating at what position vertical lines should be drawn
`helpLinesH`	boolean, indicating if horizontal lines should be drawn to indicate clusters
`ownCluster`	a vector of same length AND ORDER as data. This vector will just be cbind to the data. If provided, no kmeans clustering be calculated. For the graph, the clusters will be sorted alphabetically from bottom to top of the graph.
`showClusters`	should clusters be indicatd by colorful lines?
`tileSepColor`	color to seperate tiles by (not recommended for heatmaps with many tiles)

list with 1) a data.frame, same as "data", but with an additional column, defining the cluster for each row, 2) the data.frame used as input for the plot, 3) a ggplot object