plotCellYield {phemd} | R Documentation

## Plot cell yield of each sample as bar plot

### Description

Plots cell yield (number of viable cells) of each single-cell sample in decreasing order as horizontal bar plot

### Usage

    plotCellYield(myobj, labels = NULL, cmap = NULL, font_sz = 0.6,
      w = 8, h = 9.5)

### Arguments

`myobj` | Phmed object containing expression data for each sample in 'data' slot
`labels` | Vector containing group labels for samples (optional). If not provided, bars will be of uniform color (blue)
`cmap` | Vector containing colors by which histogram bars should be colored (optional)
`font_sz` | Scaling factor for font size of sample names in barplot
`w` | Width of plot in inches
`h` | Height of plot in inches

### Value

None

### Examples

    my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))
    my_phemdObj_lg <- removeTinySamples(my_phemdObj, 10)
    my_phemdObj_lg <- aggregateSamples(my_phemdObj_lg, max_cells=1000)
    my_phemdObj_monocle <- embedCells(my_phemdObj_lg, data_model = 'gaussianff', sigma=0.02, maxIter=2)
    my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)
    my_phemdObj_final <- clusterIndividualSamples(my_phemdObj_monocle)
    my_phemdObj_final <- generateGDM(my_phemdObj_final)
    my_EMD_mat <- compareSamples(my_phemdObj_final)
    cluster_assignments <- groupSamples(my_EMD_mat, distfun = 'hclust', ncluster=4)
    plotCellYield(my_phemdObj_final, labels=cluster_assignments, font_sz = 0.8)

[Package phemd version 1.1.1 Index]