Description Usage Arguments Examples
heatmap_nbor plot heatmap of gene expression
1 2 3 | 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)
|
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 |
plot_genes |
a vector storing the genes selected for plot, same as appeared in the row names of |
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")) |
1 2 3 4 5 6 7 8 9 10 | ## 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)
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