Package org.rosuda.JRI

Examples of org.rosuda.JRI.Rengine.eval()

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            errorMessage = "Figure height or width is too small. Minimun height and width is 500.";
            return;
          }
        }

        rEngine.eval("dataset<- matrix(\"\",nrow ="
            + newPeakList[0].length + ",ncol=" + newPeakList.length
            + ")");

        if (plegend) {
          rEngine.eval("stars<- matrix(\"\",nrow ="
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        rEngine.eval("dataset<- matrix(\"\",nrow ="
            + newPeakList[0].length + ",ncol=" + newPeakList.length
            + ")");

        if (plegend) {
          rEngine.eval("stars<- matrix(\"\",nrow ="
              + newPeakList[0].length + ",ncol="
              + newPeakList.length + ")");
        }

        // assing the values to the matrix
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            double value = newPeakList[column][row];

            if (plegend) {
              String pValue = pValueMatrix[column][row];
              rEngine.eval("stars[" + r + "," + c + "] = \""
                  + pValue + "\"");
            }

            if (!Double.isInfinite(value) && !Double.isNaN(value)) {
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                  + pValue + "\"");
            }

            if (!Double.isInfinite(value) && !Double.isNaN(value)) {

              rEngine.eval("dataset[" + r + "," + c + "] = "
                  + value);
            } else {

              rEngine.eval("dataset[" + r + "," + c + "] = NA");
            }
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              rEngine.eval("dataset[" + r + "," + c + "] = "
                  + value);
            } else {

              rEngine.eval("dataset[" + r + "," + c + "] = NA");
            }
          }
        }
        finishedPercentage = 0.4f;
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            }
          }
        }
        finishedPercentage = 0.4f;

        rEngine.eval("dataset <- apply(dataset, 2, as.numeric)");

        // Assign row names to the data set
        long rows = rEngine.rniPutStringArray(rowNames);
        rEngine.rniAssign("rowNames", rows, 0);
        rEngine.eval("rownames(dataset)<-rowNames");
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        rEngine.eval("dataset <- apply(dataset, 2, as.numeric)");

        // Assign row names to the data set
        long rows = rEngine.rniPutStringArray(rowNames);
        rEngine.rniAssign("rowNames", rows, 0);
        rEngine.eval("rownames(dataset)<-rowNames");

        // Assign column names to the data set
        long columns = rEngine.rniPutStringArray(colNames);
        rEngine.rniAssign("colNames", columns, 0);
        rEngine.eval("colnames(dataset)<-colNames");
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        rEngine.eval("rownames(dataset)<-rowNames");

        // Assign column names to the data set
        long columns = rEngine.rniPutStringArray(colNames);
        rEngine.rniAssign("colNames", columns, 0);
        rEngine.eval("colnames(dataset)<-colNames");

        finishedPercentage = 0.5f;

        // Remove the rows with too many NA's. The distances between
        // rows can't be calculated if the rows don't have
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        finishedPercentage = 0.5f;

        // Remove the rows with too many NA's. The distances between
        // rows can't be calculated if the rows don't have
        // at least one sample in common.
        rEngine.eval(" d <- as.matrix(dist(dataset))");
        rEngine.eval("d[upper.tri(d)] <- 0");
        rEngine.eval("dataset <- dataset[-na.action(na.omit(d)),]");

        finishedPercentage = 0.8f;
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        // Remove the rows with too many NA's. The distances between
        // rows can't be calculated if the rows don't have
        // at least one sample in common.
        rEngine.eval(" d <- as.matrix(dist(dataset))");
        rEngine.eval("d[upper.tri(d)] <- 0");
        rEngine.eval("dataset <- dataset[-na.action(na.omit(d)),]");

        finishedPercentage = 0.8f;

        String marginParameter = "margins = c(" + columnMargin + ","
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