plotCellYield {phemd} | R Documentation |
Plots cell yield (number of viable cells) of each single-cell sample in decreasing order as horizontal bar plot
plotCellYield(myobj, labels = NULL, cmap = NULL, font_sz = 0.6, w = 8, h = 9.5)
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 |
None
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)