plotCellYield: Plot cell yield of each sample as bar plot

In KrishnaswamyLab/phemd: Phenotypic EMD for comparison of single-cell samples

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)

KrishnaswamyLab/phemd documentation built on Oct. 2, 2024, 5:10 a.m.