public static void Run(StatisticalResultCsv item)
{
string labelFile =
$"{Config.WorkingFolder}\\{item.Method}\\{item.Dataset}\\individuals\\{item.File}";
string original_dataset = item.Dataset.Replace("_" + item.Transformation, "");
FeatureType ft = FeatureTypeExtension.FromString(item.DataType);
labels = FileExtension.Readlabels(labelFile);
//
if (item.Method.ToUpper() == "KMEDOIDS")
{
medoidIndices = labels.Distinct().OrderBy(c => c).ToArray();
}
else if (ft != FeatureType.Reactivity)
{
medoidIndices = CsMetrics.GetMedoidsByDistanceMatrix(labelFile, item.Dataset).Select(c => c.Index).ToArray();
}
else
{
medoidIndices = CsMetrics.GetMedoids(labelFile, item.Dataset).Select(c => c.Index).ToArray();
}
//medoidIndices = ft == FeatureType.Reactivity ? CsMetrics.GetMedoids(labelFile, item.Dataset).Select(c => c.Index).ToArray() : FileExtension.Readlabels(labelFile).Distinct().ToArray();
medoidIndices = medoidIndices.OrderBy(c => c).ToArray();
string rmdFile = $"{Config.WorkingFolder}\\reports\\{item.File.Replace(".csv", ".Rmd")}";
using (StreamReader templateStreamReader = new StreamReader($"{Config.WorkingFolder}\\job_report.Rmd"))
using (StreamWriter rmdStreamWriter = new StreamWriter(rmdFile))
{
while (!templateStreamReader.EndOfStream)
{
string line = templateStreamReader.ReadLine();
if (string.IsNullOrWhiteSpace(line))
{
line = string.Empty;
}
//group = read.csv("C:\\Icas.Test\\kmedoids\\length_71\\wt\\individuals\\kmedoids_k_3_round_12_labels.csv", header = FALSE)$V1
//y = read.csv("C:\\Icas.Test\\cs_efficiency\\cs_efficiency_log_wt.csv", header = FALSE)$V1
if (line.StartsWith(@"group = read.csv"))
{
line = $"group = read.csv(\"{Config.WorkingFolder.Replace("\\", "\\\\")}\\\\{item.Method}\\\\{item.Dataset}\\\\individuals\\\\{item.File}\", header = FALSE)$V1";
}
else if (line.StartsWith(@"y = read.csv"))
{
line =
$"y =read.csv(\"{Config.WorkingFolder.Replace("\\", "\\\\")}\\\\cs_efficiency\\\\cs_efficiency_log_{item.Degredome}.csv\", header = FALSE)$V1";
}
else if (line == @"#### Structure")
{
line = item.Length == 21 ? "" : GetMedoidImageString(item);
}
else if (line == "date: \"3 October 2016\"")
{
line = DateTime.Today.ToString("date: \"dd MMM yyyy\"");
}
else if (line == "csv_data = read.csv(\"cs_datasets/cs_reactivity_wt_21.csv\", sep=\",\", header = FALSE)")
{
line = $"csv_data = read.csv(\"{Config.WorkingFolder.Replace("\\", "\\\\")}/cs_datasets/cs_reactivity_{item.Degredome}_{item.Length}.csv\", sep=\",\", header = FALSE)";
}
else if (line.StartsWith("##### Reactivity_centroids"))
{
if (ft == FeatureType.Reactivity)
{
string centroidsPng = GetFilename();
Icas.Common.ProcessExtension.RunScript("job_plot2d.py",
$"{item.Dataset} {labelFile} {centroidsPng}");
line = $"##### centroids\r\n\r\n{Rmd.InsertImage(centroidsPng, "centroids")}";
}
else
{
line = "";
}
}
else if (line.StartsWith("medoids = c(63, 264, 366)"))
{
line = $"medoids = c({string.Join(", ", medoidIndices.Select(c => c.ToString()))})";
}
//csv_data = read.csv("cs_datasets/cs_structure_wt_71_distance_matrix.csv", sep=",", header = FALSE)
else if (line.StartsWith("csv_data = read.csv(\"cs_datasets/cs_structure_wt_71_distance_matrix.csv\", sep=\",\", header = FALSE)"))
{
line = $"csv_data = read.csv(\"{Config.WorkingFolder.Replace("\\", "/")}cs_datasets/cs_structure_{item.Degredome}_{item.Length}_distance_matrix.csv\", sep=\",\", header = FALSE)";
}
rmdStreamWriter.WriteLine(line);
}
templateStreamReader.Close();
rmdStreamWriter.Flush();
rmdStreamWriter.Close();
}
Rmd.ToHtml(rmdFile);
}
private static string GetMedoidImageString(StatisticalResultCsv item)
{
try
{
//string labelFile = $"{Config.WorkingFolder}\\{item.Method}\\{item.Dataset}\\individuals\\{item.File}";
DegradomeType dt;
Enum.TryParse(item.Degredome, out dt);
FeatureType ft = FeatureTypeExtension.FromString(item.DataType);
double[,] X = Ezfx.Csv.Ex.CsvMatrix.Read($"{Config.WorkingFolder}\\cs_datasets\\{item.Dataset}.csv");
//if (item.Method.ToUpper() == "KMEDOIDS")
//{
// medoidIndices = labels.Distinct().OrderBy(c => c).ToArray();
//}
//else if (ft != FeatureType.Reactivity)
//{
// medoidIndices = CsMetrics.GetMedoidsByDistanceMatrix(labelFile, item.Dataset).Select(c => c.Index).ToArray();
//}
//else
//{
// medoidIndices = CsMetrics.GetMedoids(labelFile, item.Dataset).Select(c => c.Index).ToArray();
//}
//medoidIndices = ft == FeatureType.Reactivity ? CsMetrics.GetMedoids(labelFile, item.Dataset).Select(c => c.Index).ToArray() : FileExtension.Readlabels(labelFile).Distinct().ToArray();
string medoidImageString = "#### Structure\r\n\r\nFor clustering algorithms using reactivity, the structure is for reference only .\r\n\r\n";
int index = 0;
string[] centerBitmapFiles = new string[medoidIndices.Length];
string[] annotation = new string[medoidIndices.Length];
for (int i = 0; i < medoidIndices.Length; i++)
{
centerBitmapFiles[i] =
$"{Config.CsStrucFolder}\\plot\\{dt}_{item.Length}_{medoidIndices[i]}.png";
annotation[i] = $"Medoid {i}";
}
if (ft == FeatureType.RnaDistance)
{
double[,] medoidDistanceMatrix = Clustering.Metrics.GetSubDistanceMatrix(X, medoidIndices);
medoidImageString += Rmd.StartRBlock("distance_matrx");
medoidImageString += Rmd.PrintMatrix(medoidDistanceMatrix);
medoidImageString += Rmd.EndRBlock();
if (medoidIndices.Length == 3)
{
string guid = Guid.NewGuid().ToString().Replace("-", "_");
string file = $"{Config.WorkingFolder}\\reports\\figure\\{guid}.png";
ImageHelper.DistanceTriangle(file, centerBitmapFiles, MathEx.DistanceMatrixToTriangle(medoidDistanceMatrix));
medoidImageString += Rmd.InsertImage(file, "distance");
}
}
int[][] samples = Metrics.Sample(labels, 20);
for (int i = 0; i < medoidIndices.Length; i++)
{
medoidImageString += $"##### Centre of Cluster {index} (Data Point {medoidIndices[i]})\r\n\r\n";
medoidImageString += Rmd.InsertImage(centerBitmapFiles[i], "Cleavage site structure");
if (ft == FeatureType.RnaDistance)
{
string thumbFile = GetFilename();
medoidImageString += $"Other structures of the this group:\r\n\r\n";
medoidImageString += $"![Cleavage site structure]({thumbFile.Replace("\\", "\\\\")})\r\n\r\n";
GenerateGroupThumbnails(thumbFile, item, samples[i]);
//star
if (medoidIndices.Length == 3)
{
medoidImageString += $"examine the first of the above:\r\n\r\n";
string starFile = GetFilename();
medoidImageString += $"![Cleavage site structure]({starFile.Replace("\\", "\\\\")})\r\n\r\n";
int first = samples[i][0];
ImageHelper.Star(starFile,
$"{Config.WorkingFolder}\\cs_rna_struct\\plot\\{item.Degredome}_{item.Length}_{first + 1}.png",
$"CS {first + 1}",
centerBitmapFiles, annotation,
new float[] { (float)X[first, medoidIndices[0]], (float)X[first, medoidIndices[1]], (float)X[first, medoidIndices[2]] }
);
}
}
index++;
}
return(medoidImageString);
}
catch (NotImplementedException)
{
//throw;
return(string.Empty);
}
}
