Description Usage Arguments Examples
SC_hc_colorCode hierarchical clustering of single cells, leaves color-coded by cell type information.
1 2 3 |
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" |
1 2 3 4 5 6 7 8 9 | ## 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)
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