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PlotRoutines.cs
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PlotRoutines.cs
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using Accord.Statistics.Filters;
using Microsoft.Office.Core;
using System;
using System.Collections.Generic;
using System.Data;
using System.Linq;
using Excel = Microsoft.Office.Interop.Excel;
namespace GINtool
{
public static class PlotRoutines
{
public static Excel.Application theApp = null;
static double estimatedFontSize(int nritems)
{
return -Math.Log10(nritems) + 2.6021;
}
static int fontsize(int nritems)
{
int size = (int)Math.Pow(10, estimatedFontSize(nritems));
if (size < 2)
size = 2;
if (size > 10)
size = 10;
return size;
}
public static Excel.Chart CreateDistributionPlot(List<double> sortedFC, List<int> sortedIndex, string chartName)
{
if (theApp == null)
return null;
Excel.Worksheet aSheet = theApp.Worksheets.Add();
Excel.ChartObjects xlCharts = (Excel.ChartObjects)aSheet.ChartObjects(Type.Missing);
Excel.ChartObject myChart = (Excel.ChartObject)xlCharts.Add(10, 80, 500, 500);
Excel.Chart chartPage = myChart.Chart;
//chartPage.ChartType = Excel.XlChartType.xlXYScatter;
chartPage.ChartType = Excel.XlChartType.xlColumnClustered;
var series = (Excel.SeriesCollection)chartPage.SeriesCollection();
var aSerie = series.NewSeries();
aSerie.Name = String.Format("Serie {0}", 1);
//aSerie.ChartType = Excel.XlChartType.xlXYScatter;
//aSerie.XValues = sortedIndex.ToArray();
aSerie.Values = sortedFC.ToArray();
//distributionChart.Palette = (ChartColorPalette)Properties.Settings.Default.defaultPalette;
//distributionChart.Titles.Add("distribution plot");
var yAxis = (Excel.Axis)chartPage.Axes(Excel.XlAxisType.xlCategory, Excel.XlAxisGroup.xlPrimary);
yAxis.HasTitle = true;
yAxis.AxisTitle.Text = "index (sorted)";
var xAxis = (Excel.Axis)chartPage.Axes(Excel.XlAxisType.xlValue, Excel.XlAxisGroup.xlPrimary);
xAxis.HasTitle = true;
xAxis.AxisTitle.Text = "fold-change";
chartPage.Axes(Excel.XlAxisType.xlCategory).TickLabelPosition = Excel.XlTickLabelPosition.xlTickLabelPositionNone;
chartPage.Axes(Excel.XlAxisType.xlValue).MajorGridLines.Delete();
chartPage.Legend.Delete();
chartPage.ChartTitle.Delete();
chartPage.Location(Excel.XlChartLocation.xlLocationAsNewSheet, chartName);
aSheet.Delete();
return chartPage;
}
public static Excel.Chart CreateRankingPlot(Excel.Worksheet aSheet, List<element_rank> element_Ranks, string chartName)
{
if (theApp == null)
return null;
string sheetName = chartName.Replace("Plot_", "Tab_");
aSheet.Name = sheetName;
Excel.ChartObjects xlCharts = (Excel.ChartObjects)aSheet.ChartObjects(Type.Missing);
Excel.ChartObject myChart = (Excel.ChartObject)xlCharts.Add(10, 80, 500, 500);
Excel.Chart chartPage = myChart.Chart;
chartPage.ChartType = Excel.XlChartType.xlXYScatter;
var series = (Excel.SeriesCollection)chartPage.SeriesCollection();
int offset = 3;
List<int> __offset = new List<int>() { offset };
int[] _offset = element_Ranks.Select(w => offset += w.nr_genes.Length).ToArray();
__offset.AddRange(_offset);
int[] offsets = __offset.GetRange(0, element_Ranks.Count).ToArray();
for (int i = element_Ranks.Count - 1; i >= 0; i--)
{
element_rank eRank = element_Ranks[i];
var xy1 = series.NewSeries();
xy1.Name = eRank.catName;
xy1.ChartType = Excel.XlChartType.xlBubble3DEffect;
int nrGenes = eRank.nr_genes.Length;
if (eRank.mad_fc != null && nrGenes > 0)
{
xy1.XValues = string.Format("={0}!$C${1}:$C${2}", sheetName, offsets[i], nrGenes + offsets[i] - 1); //element_rank.value.average_fc;
xy1.Values = string.Format("={0}!$D${1}:$D${2}", sheetName, offsets[i], nrGenes + offsets[i] - 1); //element_rank.value.mad_fc;
xy1.BubbleSizes = string.Format("={0}!$B${1}:$B${2}", sheetName, offsets[i], nrGenes + offsets[i] - 1); //element_rank.value.nr_genes;
xy1.HasDataLabels = true;
dynamic dataLabels = xy1.DataLabels();
dataLabels.Format.TextFrame2.TextRange.InsertChartField(MsoChartFieldType.msoChartFieldRange, string.Format("={0}!$A${1}:$A${2}", sheetName, offsets[i], nrGenes + offsets[i] - 1));
dataLabels.ShowRange = true;
dataLabels.ShowValue = false;
offset += nrGenes;
}
}
//foreach (var element_rank in element_Ranks.Select((value, index) => new { value, index }))
//{
// }
//}
chartPage.Axes(Excel.XlAxisType.xlValue).TickLabelPosition = Excel.XlTickLabelPosition.xlTickLabelPositionNone;
chartPage.Axes(Excel.XlAxisType.xlValue).MajorGridLines.Delete();
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.Weight = 0.25;
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.DashStyle = Excel.XlLineStyle.xlDashDot;
chartPage.Legend.Delete();
chartPage.ChartColor = 22;
chartPage.Location(Excel.XlChartLocation.xlLocationAsNewSheet, chartName);
return chartPage;
}
public static Excel.Chart CreateRankingPlot2(List<element_rank> element_Ranks, string chartName, bool bestPlot = false, bool bestNew = false)
{
if (theApp == null)
return null;
if (theApp == null)
return null;
Excel.Worksheet aSheet = theApp.Worksheets.Add();
//string sheetName = chartName.Replace("PlotBest_", "TabBest_");
//aSheet.Name = sheetName;
Excel.ChartObjects xlCharts = (Excel.ChartObjects)aSheet.ChartObjects(Type.Missing);
Excel.ChartObject myChart = (Excel.ChartObject)xlCharts.Add(10, 80, 500, 500);
Excel.Chart chartPage = myChart.Chart;
chartPage.ChartType = Excel.XlChartType.xlXYScatter;
var series = (Excel.SeriesCollection)chartPage.SeriesCollection();
int offset = 3;
List<int> __offset = new List<int>() { offset };
int[] _offset = element_Ranks.Select(w => offset += w.nr_genes.Length).ToArray();
__offset.AddRange(_offset);
int[] offsets = __offset.GetRange(0, element_Ranks.Count).ToArray();
for (int i = element_Ranks.Count - 1; i >= 0; i--)
{
element_rank eRank = element_Ranks[i];
var xy1 = series.NewSeries();
xy1.Name = eRank.catName;
xy1.ChartType = Excel.XlChartType.xlBubble3DEffect;
int nrGenes = eRank.nr_genes.Length;
if (eRank.mad_fc != null && nrGenes > 0)
{
if (bestPlot & bestNew)
{
xy1.XValues = eRank.best_genes_percentage;
xy1.Values = eRank.average_fc;
}
else
{
xy1.XValues = eRank.average_fc;
xy1.Values = eRank.mad_fc;
}
xy1.BubbleSizes = eRank.nr_genes;
xy1.HasDataLabels = true;
dynamic dataLabels = xy1.DataLabels();
for (int g = 0; g < eRank.nr_genes.Length; g++)
{
Excel.Point _point = xy1.Points(g + 1);
_point.DataLabel.Text = eRank.genes[g];
}
dataLabels.ShowRange = true;
dataLabels.ShowValue = false;
offset += nrGenes;
}
}
myChart.Chart.ChartGroups(1).BubbleScale = 50;
chartPage.Axes(Excel.XlAxisType.xlValue).HasTitle = true;
chartPage.Axes(Excel.XlAxisType.xlCategory).HasTitle = true;
string xLabel = (bestPlot & bestNew) ? "% logical regulation" : (bestPlot ? "average signed FC" : "average FC");
string yLabel = (bestPlot & bestNew) ? "average FC" : (bestPlot ? "mad abs(FC)" : "mad FC");
chartPage.Axes(Excel.XlAxisType.xlCategory).AxisTitle.Text = xLabel;
chartPage.Axes(Excel.XlAxisType.xlValue).AxisTitle.Text = yLabel;
chartPage.Axes(Excel.XlAxisType.xlValue).TickLabelPosition = Excel.XlTickLabelPosition.xlTickLabelPositionNone;
chartPage.Axes(Excel.XlAxisType.xlValue).MajorGridLines.Delete();
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.Weight = 0.25;
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.DashStyle = Excel.XlLineStyle.xlDashDot;
chartPage.Legend.Delete();
chartPage.ChartColor = (bestPlot | bestNew) ? 21 : 22;
chartPage.Location(Excel.XlChartLocation.xlLocationAsNewSheet, chartName);
aSheet.Delete();
return chartPage;
}
public static Excel.Chart CreateVolcanoPlot (List<element_rank> element_Ranks, string chartName)
{
if (theApp == null)
return null;
if (theApp == null)
return null;
Excel.Worksheet aSheet = theApp.Worksheets.Add();
Excel.ChartObjects xlCharts = (Excel.ChartObjects)aSheet.ChartObjects(Type.Missing);
Excel.ChartObject myChart = (Excel.ChartObject)xlCharts.Add(10, 80, 500, 500);
Excel.Chart chartPage = myChart.Chart;
chartPage.ChartType = Excel.XlChartType.xlXYScatter;
var series = (Excel.SeriesCollection)chartPage.SeriesCollection();
int offset = 3;
List<int> __offset = new List<int>() { offset };
int[] _offset = element_Ranks.Select(w => offset += w.nr_genes.Length).ToArray();
__offset.AddRange(_offset);
int[] offsets = __offset.GetRange(0, element_Ranks.Count).ToArray();
for (int i = element_Ranks.Count - 1; i >= 0; i--)
{
element_rank eRank = element_Ranks[i];
var xy1 = series.NewSeries();
xy1.Name = eRank.catName;
xy1.ChartType = Excel.XlChartType.xlBubble3DEffect;
int nrGenes = eRank.nr_genes.Length;
if (eRank.mad_fc != null && nrGenes > 0)
{
xy1.XValues = eRank.average_fc;
xy1.Values = eRank.p_fdr;
xy1.BubbleSizes = eRank.nr_genes; //Enumerable.Repeat(10, eRank.nr_genes.Length).ToArray();
xy1.HasDataLabels = true;
dynamic dataLabels = xy1.DataLabels();
for (int g = 0; g < eRank.nr_genes.Length; g++)
{
Excel.Point _point = xy1.Points(g + 1);
_point.DataLabel.Text = eRank.genes[g];
}
dataLabels.ShowRange = true;
dataLabels.ShowValue = false;
offset += nrGenes;
}
}
myChart.Chart.ChartGroups(1).BubbleScale = 50;
chartPage.Axes(Excel.XlAxisType.xlValue).HasTitle = true;
chartPage.Axes(Excel.XlAxisType.xlCategory).HasTitle = true;
string xLabel = "average signed FC";
string yLabel = "-log(P)";
chartPage.Axes(Excel.XlAxisType.xlCategory).AxisTitle.Text = xLabel;
chartPage.Axes(Excel.XlAxisType.xlValue).AxisTitle.Text = yLabel;
chartPage.Axes(Excel.XlAxisType.xlValue).TickLabelPosition = Excel.XlTickLabelPosition.xlTickLabelPositionNextToAxis;
chartPage.Axes(Excel.XlAxisType.xlValue).MajorGridLines.Delete();
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.Weight = 0.25;
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.DashStyle = Excel.XlLineStyle.xlDashDot;
chartPage.Legend.Delete();
chartPage.ChartColor = 10;
chartPage.Location(Excel.XlChartLocation.xlLocationAsNewSheet, chartName);
aSheet.Delete();
return chartPage;
}
public static Excel.Chart CreateCategoryPlot(element_fc element_Fcs, string chartName)
{
if (theApp == null)
return null;
Excel.Worksheet aSheet = theApp.Worksheets.Add();
Excel.ChartObjects xlCharts = (Excel.ChartObjects)aSheet.ChartObjects(Type.Missing);
Excel.ChartObject myChart = (Excel.ChartObject)xlCharts.Add(10, 80, 500, 500);
Excel.Chart chartPage = myChart.Chart;
chartPage.ChartType = Excel.XlChartType.xlXYScatter;
var series = (Excel.SeriesCollection)chartPage.SeriesCollection();
int nrCategories = element_Fcs.All.Count;
double MMAX = 0;
double MMIN = 0;
for (int _i = 0; _i < nrCategories; _i++)
{
if (element_Fcs.All[_i].p_values != null && element_Fcs.All[_i].p_values.Length > 0)
{
if (element_Fcs.All[_i].fc_values.Min() < MMIN)
MMIN = element_Fcs.All[_i].fc_values.Min();
if (element_Fcs.All[_i].fc_values.Max() > MMAX)
MMAX = element_Fcs.All[_i].fc_values.Max();
}
}
foreach (var element_Fc in element_Fcs.All.Select((value, index) => new { value, index }))
{
var xy1 = series.NewSeries();
xy1.Name = element_Fc.value.catName;
xy1.ChartType = Excel.XlChartType.xlXYScatter;
if (element_Fc.value.fc_values != null && element_Fc.value.fc_values.Length > 0)
{
xy1.XValues = element_Fc.value.fc_values;
xy1.Values = Enumerable.Repeat(element_Fc.index + 0.5, element_Fc.value.fc_values.Length).ToArray();
xy1.MarkerStyle = Excel.XlMarkerStyle.xlMarkerStyleNone;
xy1.MarkerSize = 2;
//xy1.ErrorBar(Excel.XlErrorBarDirection.xlY, Excel.XlErrorBarInclude.xlErrorBarIncludeBoth, Excel.XlErrorBarType.xlErrorBarTypeFixedValue, 0.1);
xy1.ErrorBar(Excel.XlErrorBarDirection.xlY, Excel.XlErrorBarInclude.xlErrorBarIncludeBoth, Excel.XlErrorBarType.xlErrorBarTypeFixedValue, 0.4);
Excel.ErrorBars errorBars = xy1.ErrorBars;
errorBars.EndStyle = Excel.XlEndStyleCap.xlNoCap;
errorBars.Format.Line.Weight = 1.25f;
// give each serie different color
switch (element_Fc.index % 6)
{
case 0:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent1;
break;
case 1:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent2;
break;
case 2:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent3;
break;
case 3:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent4;
break;
case 4:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent5;
break;
case 5:
errorBars.Format.Line.ForeColor.ObjectThemeColor = MsoThemeColorIndex.msoThemeColorAccent6;
break;
}
//Excel.Points sPoints = xy1.Points();
////xy1.HasDataLabels = true;
////For every row in the values table, plot the date against the variable value
//for (int p = 0; p < element_Fc.value.fc.Count(); p++)
//{
// Excel.Point lPoint = sPoints.Item(p + 1);
// //lPoint.Name = "P" + p.ToString();
// //myChart.Series[Variable].Points.AddXY(Convert.ToDateTime(row["Date"].ToString()), row["Variable"].ToString());
// lPoint.HasDataLabel = true;
// lPoint.DataLabel.Text = "P" + p.ToString(); // " = #VALY \r\nDate = #VALX{d} \r\np = "+ p.ToString();
// lPoint.DataLabel.Font.Size = 2;
// //Excel.Point lPoint = sPoints.Item(p);
// //points += 1;
//}
}
var yAxis = (Excel.Axis)chartPage.Axes(Excel.XlAxisType.xlValue, Excel.XlAxisGroup.xlPrimary);
//yAxis.AxisTitle.Text = "Regulon";
Excel.TickLabels labels = yAxis.TickLabels;
labels.Offset = 1;
}
chartPage.ChartColor = 1; // Properties.Settings.Default.defaultPalette;
// as a last step, add the axis labels series
if (true)
{
var xy2 = series.NewSeries();
xy2.ChartType = Excel.XlChartType.xlXYScatter;
//# Excel.Range rng = (Excel.Range)_tmpSheet.Range[_tmpSheet.Cells[3, (i*2)+1], _tmpSheet.Cells[6, (i * 2) + 1]];
xy2.XValues = Enumerable.Repeat(MMIN, nrCategories).ToArray();
//rng = (Excel.Range)_tmpSheet.Range[_tmpSheet.Cells[3, (i * 2) + 2], _tmpSheet.Cells[6, (i * 2) + 2]];
float[] yv = new float[nrCategories];
for (int _i = 0; _i < nrCategories; _i++)
{
yv[_i] = ((float)_i) + 0.5f;
}
xy2.Values = yv;
xy2.MarkerStyle = Excel.XlMarkerStyle.xlMarkerStyleNone;
xy2.HasDataLabels = true;
for (int _i = 0; _i < nrCategories; _i++)
{
xy2.DataLabels(_i + 1).Text = element_Fcs.All[_i].catName;
}
xy2.DataLabels().Position = Excel.XlDataLabelPosition.xlLabelPositionLeft;
xy2.DataLabels().Font().Size = fontsize(element_Fcs.All.Count);
}
chartPage.Axes(Excel.XlAxisType.xlValue).TickLabelPosition = Excel.XlTickLabelPosition.xlTickLabelPositionNone;
chartPage.Axes(Excel.XlAxisType.xlValue).MajorGridLines.Delete();
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.Weight = 0.25;
chartPage.Axes(Excel.XlAxisType.xlValue).Format.Line.DashStyle = Excel.XlLineStyle.xlDashDot;
chartPage.Axes(Excel.XlAxisType.xlValue).MaximumScale = nrCategories;
chartPage.Axes(Excel.XlAxisType.xlValue).MinimumScale = 0;
chartPage.Legend.Delete();
chartPage.Location(Excel.XlChartLocation.xlLocationAsNewSheet, chartName);
aSheet.Delete();
return chartPage;
}
public static (float, float) CalculateStepSize(float range, float targetSteps)
{
// calculate an initial guess at step size
float tempStep = range / targetSteps;
// get the magnitude of the step size
float mag = (float)Math.Floor(Math.Log10(tempStep));
float magPow = (float)Math.Pow(10, mag);
// calculate most significant digit of the new step size
float magMsd = (int)(tempStep / magPow + 0.5);
// promote the MSD to either 1, 2, or 5
if (magMsd > 5.0)
magMsd = 10.0f;
else if (magMsd > 2.0)
magMsd = 5.0f;
else if (magMsd > 1.0)
magMsd = 2.0f;
return (magMsd * magPow, magMsd);
}
}
}