heatmap_nbor: heatmap_nbor plot heatmap of gene expression

Description Usage Arguments Examples

Description

heatmap_nbor plot heatmap of gene expression

Usage

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heatmap_nbor(exprs, cell_order, plot_genes, cell_annotation,
  num_gene_cluster = 4, hm_height = 10, hm_width = 10, baseName,
  colorPalette = NULL, n_linechart = NULL)

Arguments

exprs

a data frame or matrix of expression data(ie. rpkm, TPM, fpkm) containing cells in columns and genes in rows

cell_order

a vector storing the order of cells with cell ID or name, same as appeared in column names of exprs

plot_genes

a vector storing the genes selected for plot, same as appeared in the row names of exprs

cell_annotation

a two column data frame or matrix annotating cells(cell ID or name) with cell types

num_gene_cluster

a integer indicating the number of gene clusters to generate by cutting the dendrogram tree, if num_gene_cluster = NULL, no gene clusters will be generated

hm_height

an integeter to specify the heatmap height

hm_width

an integeter to specify heatmap width

baseName

a character string to specify the prefix of name of result files

colorPalette

a character vector to specify the color scheme of column side bar that labels cell type of individual cells. Default value is NULL, a default color scheme will be deployed. Alternatively users can specfiy their desired color paletter, for examples, colorPalette=c("red","green","blue","black","orange","purple","burlywood4")

n_linechart

a string vector to specify for which cell ordering to plot the line chart. Default value is NULL, all the cells in cell_order will be plot. Alternatively, users could specify, for examples two line charts, by n_linechart = list(c("cell1","cell2"),c("cell3","cell4"))

Examples

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## Not run: 
heatmap_nbor(exprs = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup.txt",                        
             cell_order = "CDP_2_CDP_1_preDC_9_preDC_3_order.txt", 
             plot_genes = "CDP_2_CDP_1_preDC_9_preDC_3_vgam_deg0.05.txt",
             cell_annotation = "sample_GSE60783_noOutlier.txt", 
             num_gene_cluster = 6,
             hm_height = 15, hm_width = 10,
             baseName = "CDP_2_CDP_1_preDC_9_preDC_3_order_vgam_deg0.05") 

## End(Not run)

dynverse/Mpath documentation built on May 14, 2019, 8:42 a.m.