test_pipeline.R

In angy89/TinderMIX: TinderMIX: An R package to cluster gene expression by contour plots

library(TinderMIX)

pheno = read.delim("sample_data/WY-14643_pheno.txt")
exp_data = read.delim("sample_data/WY-14643_exp.txt")
drugName = "WY-14643"
fc_data = TinderMIX::compute_fc(exp_data = exp_data,pheno_data = pheno,dose_index = 2,time_index = 4)

responsive_genes = rownames(fc_data$fc_data)[1:100]
exp_data = fc_data$fc_data
pheno_data = fc_data$pdata

source("sample_data/set_parameters.R")

contour_res = suppressMessages(TinderMIX::create_contour(exp_data, pheno_data, 
																							responsive_genes,
																							dose_index = dose_index,
																							time_point_index = time_point_index ,
																							gridSize = gridSize,
																							pvalFitting = pvalFitting,
																							pvalFitting.adj.method = pvalFitting.adj.method,
																							logScale = T, modelSelection = 1:3))

print("Step 4: Run BMD_IC50 analysis on every gene")
DDRGene = TinderMIX::run_all_BMD_IC50(contour_res = contour_res,
											 activity_threshold = activity_threshold,  
											 BMD_response_threshold = BMD_response_threshold, 
											 mode=mode, 
											 nDoseInt=nDoseInt, nTimeInt=nTimeInt, 
											 doseLabels = doseLabels, timeLabels = timeLabels,
											 tosave=FALSE, addLegend = FALSE, path = ".",
											 relGenes = contour_res$ggenes, toPlot = FALSE)

plot_dynamic_dose_responsive_map(contour_res, geneName="Gad1",activity_threshold,
																						BMD_response_threshold,mode,nTimeInt,nDoseInt,
																						timeLabels,doseLabels)

# plot heatmap with number of genes for each label
# source("R/plotting_functions.R")
gene_plot = TinderMIX::plot_number_genes_labels(res = DDRGene,drugName = drugName,timeLabels = timeLabels,doseLabels = doseLabels)
plot(gene_plot)

# plot radial plots with number of genes for the 12 combination of dose and time points
label_plot = TinderMIX::plot_cake_diagrams_time_dose_effect(res = DDRGene, timeLabels = timeLabels,doseLabels = doseLabels)

res = TinderMIX::create_gene_table(DDRGene,contour_res, nTimeInt,nDoseInt,biomart_dataset = "rnorvegicus_gene_ensembl")

# hls_res = hls_genes_clustering(contour_res$GenesMap, nClust = c(5,10,15,20,25), method="pearson", hls.method = "ward")
# 
# clpr = create_prototypes(clust_res=hls_res,contour_res=contour_res,optcl = hls_res$clusterList[[5]], mode = "mean") #summaryMat
# 	
# plot_clusters_prototypes(meanXYZ = clpr$meanXYZ)
#