SC_hc_colorCode: SC_hc_colorCode hierarchical clustering of single cells,...

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

SC_hc_colorCode hierarchical clustering of single cells, leaves color-coded by cell type information.

Usage

SC_hc_colorCode(dataFile, baseName = NULL, cuttree_k = NULL,
  sampleFile = NULL, width = 22, height = 10, iflog2 = TRUE,
  colorPalette = NULL, distMethod = "Euclidean")

Arguments

dataFile	a tab delimited txt file of expression data, columns are cells, rows are genes.
baseName	prefix name of resulting files
cuttree_k	number of clusters to be generated by cutting the dendrogram. cuttree_k can be an integer or NULL. If NULL, no clusters will be generated.
sampleFile	a tab delimited txt file of cell annotation, the first column is cell ID, the second column is group ID.
width	width of the resulting figure
height	height of the resulting figure
iflog2	a boolean value indiciating if the expression data will be log2 transformed.
colorPalette	if NULL, brewer.pal(n,"Set2") will be used, or colorPalette can be c("red","green","blue").
distMethod	distMethod can be one of "pearson", "kendall", "spearman" or "Euclidean"

Examples

## Not run: 
dataFile = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG.txt";
SC_hc_colorCode(dataFile = dataFile,
               cuttree_k = 11,
               sampleFile= "sample_GSE60783_noOutlier.txt",
               width = 22, height = 10, iflog2 = TRUE,
               colorPalette = c("red","green","blue"))

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.