plotCellYield: Plot cell yield of each sample as bar plot

Description Usage Arguments Value Examples

View source: R/functions-plotting.R

Description

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

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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)

phemd documentation built on Nov. 8, 2020, 8:15 p.m.