| Previous changeset 1:4d5f798a7a18 (2018-10-25) Next changeset 3:773a24b240e1 (2019-02-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1 |
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modified:
macros.xml mz_images.xml test-data/112_auto_combined_QC.pdf test-data/123_combined.RData test-data/123_combined_QC.pdf test-data/12_combined.RData test-data/12_combined_QC.pdf test-data/2123_auto_combined.RData test-data/2123_auto_combined_QC.pdf test-data/Plot_empty_spectra.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/features_test2.tabular test-data/features_test4.tabular test-data/features_test6.tabular test-data/features_test7.tabular test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/pca_imzml.pdf test-data/pixel_out2.tabular test-data/pixel_out3.tabular test-data/preprocessing_results1.pdf test-data/preprocessing_results2.pdf test-data/preprocessing_results3.pdf test-data/preprocessing_results4.pdf test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf test-data/rdata_notfiltered.pdf test-data/scores_pca.tabular test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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added:
test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/123_annotation.ibd test-data/123_annotation.imzml test-data/123_auto_combined.imzml.txt test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/123_combined_auto.tabular test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt |
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removed:
test-data/112_auto_combined.RData test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/analyze_originaloutput.RData test-data/analyze_originaloutput2.RData test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered4.RData test-data/imzml_filtered5.RData test-data/loadings_pca.tabular test-data/preprocessed.rdata test-data/preprocessing_results1.RData test-data/preprocessing_results1.txt test-data/preprocessing_results2.RData test-data/preprocessing_results2.txt test-data/preprocessing_results3.RData test-data/preprocessing_results4.RData test-data/preprocessing_results4.txt test-data/preprocessing_results5.txt test-data/rdata_notfiltered.RData |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca macros.xml --- a/macros.xml Thu Oct 25 07:27:54 2018 -0400 +++ b/macros.xml Fri Feb 15 10:20:01 2019 -0500 |
| [ |
| @@ -69,25 +69,92 @@ ## Range y coordinates minimumy = min(coord(msidata)[,2]) maximumy = max(coord(msidata)[,2]) + + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy)) + + property_df = data.frame(properties, values) + ]]></token> + + <token name="@READING_MSIDATA_INRAM@"><![CDATA[ + ## importing MSI data files + + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + + #if $infile.ext == 'imzml' + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + centroided(msidata) = $centroids + #else + msidata <- readImzML('infile') + centroided(msidata) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile') + centroided(msidata) = $centroids + #else + msidata = loadRData('infile.RData') + #end if + + ]]></token> + + <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ +########################### QC numbers ######################## +## including intensity calculations which need data in RAM + ## Number of features (mz) + maxfeatures = length(features(msidata)) + ## Range mz + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount = length(pixels(msidata)) + ## Range x coordinates + minimumx = min(coord(msidata)[,1]) + maximumx = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy = min(coord(msidata)[,2]) + maximumy = max(coord(msidata)[,2]) ## Range of intensities minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2) maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2) ## Number of intensities > 0, for if conditions npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE) + ## Number of NA in spectra matrix + NAcount = sum(is.na(spectra(msidata)[])) + ## Number of NA in spectra matrix + infcount = sum(is.infinite(spectra(msidata)[])) properties = c("Number of m/z features", "Range of m/z values", "Number of pixels", "Range of x coordinates", "Range of y coordinates", - "Range of intensities") + "Range of intensities", + "Number of NA intensities", + "Number of Inf intensities") values = c(paste0(maxfeatures), paste0(minmz, " - ", maxmz), paste0(pixelcount), paste0(minimumx, " - ", maximumx), paste0(minimumy, " - ", maximumy), - paste0(minint, " - ", maxint)) + paste0(minint, " - ", maxint), + paste0(NAcount), + paste0(infcount)) property_df = data.frame(properties, values) ]]></token> @@ -144,9 +211,9 @@ <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - Optional file with pixel coordinates and annotation: - - Tabular file: One column with x values, one column wiht y values and one column with annotations + - Tabular file: One column with x values, one column with y values and one column with annotations - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - - Pixel with coordinates outside the coordinates of the input file are ignored + - Pixel with coordinates outside the coordinates of the input file are ignored :: @@ -161,9 +228,9 @@ <xml name="reading_msidata"> <param name="infile" type="data" format="imzml,rdata,analyze75" - label="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" - help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> - <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> + label="MSI data" + help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/> + <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> <conditional name="processed_cond"> <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> <option value="no_processed" selected="True">no</option> |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca mz_images.xml --- a/mz_images.xml Thu Oct 25 07:27:54 2018 -0400 +++ b/mz_images.xml Fri Feb 15 10:20:01 2019 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1"> +<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2"> <description> mass spectrometry imaging m/z heatmaps </description> @@ -58,9 +58,9 @@ ############################# II) images #################################### -### only plot images when file has peaks and valid input m/z: +### only plot images when file has features and pixels: -if (npeaks > 0){ +if (ncol(msidata)>0 & nrow(msidata) >0){ if (length(inputmz) != 0){ for (mass in 1:length(inputmz)){ @@ -70,7 +70,7 @@ print("standard image") print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", - smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), + smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.2*maximumy,minimumy-1), main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} @@ -83,7 +83,7 @@ print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", - colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy), + colorkey=$colorkey,ylim=c(maximumy+0.2*maximumy,minimumy-1), main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} #elif str($strip) =="FALSE": @@ -100,16 +100,38 @@ ## optional svg output with original coordinates #if $svg_pixelimage: print("svg pixel image") + ## reverse y axis for svg output = correct order and nice svg image + coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 svg(file="svg_pixel_output.svg") par(mar=c(0,0,0,0)) - image(msidata, mz = inputmz[1],strip=FALSE, ylim=c(maximumy, minimumy), plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing") + image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing") dev.off() #end if + ## optional overlay all input m/z in one image + #if str($overlay_cond.overlay_selection) == "yes_overlay": + + #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours]) + colourvector = c($color_string) + + image(msidata, mz=inputmz, + plusminus = $plusminus_dalton, + col=colourvector, + contrast.enhance = "$image_contrast", + normalize.image="linear", + smooth.image = "$image_smoothing", + superpose=TRUE, main="overlay of all m/z", + ylim= c(maximumy+0.2*maximumy,minimumy-1)) + + legend("topright", + fill=colourvector, + legend=as.numeric(sort(as.character(inputmz)))) + #end if + } else {print("The input m/z were invalid")} dev.off() }else{ - print("inputfile has no intensities > 0") + print("input file has no features or pixels left") dev.off() } @@ -138,9 +160,27 @@ <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image" label="Standard image" help="No: lattice function is used to display image"/> <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/> + <conditional name="overlay_cond"> + <param name="overlay_selection" type="select" label="Overlay image"> + <option value="no_overlay" selected="True">no</option> + <option value="yes_overlay">yes</option> + </param> + <when value="no_overlay"/> + <when value="yes_overlay"> + <repeat name="colours" title="Colours for the plots" min="1" max="50"> + <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of m/z in tabular file"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + </conditional> </inputs> <outputs> - <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}"/> + <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/> <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg"> <filter>svg_pixelimage</filter> </data> @@ -174,7 +214,7 @@ <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/> </test> <test> - <param name="infile" value="preprocessed.rdata" ftype="rdata"/> + <param name="infile" value="preprocessed.RData" ftype="rdata"/> <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> <param name="name_column" value="2"/> |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/112_auto_combined.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/112_auto_combined.imzml Fri Feb 15 10:20:01 2019 -0500 |
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|
| b |
| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/features_test4.tabular --- a/test-data/features_test4.tabular Thu Oct 25 07:27:54 2018 -0400 +++ b/test-data/features_test4.tabular Fri Feb 15 10:20:01 2019 -0500 |
| b |
| b'@@ -1,101 +1,101 @@\n 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\t0.001177\t0.025661\t0.036479\n+922.319458007812\t3\tA\t0.001163\t0.035058\t0.049004\n+945.825500488281\t3\tA\t0.001163\t0.035839\t0.039942\n+914.429443359375\t3\tA\t0.001148\t0.021433\t0.032258\n+934.364013671875\t3\tA\t0.00112\t0.026118\t0.02779\n+945.788757324219\t3\tA\t0.001114\t0.060266\t0.067849\n+930.27978515625\t3\tA\t0.001111\t0.054857\t0.054186\n+987.41015625\t3\tA\t0.001091\t0.025902\t0.034883\n+917.320922851562\t3\tB\t0.001088\t-0.038094\t-0.085973\n+961.388977050781\t3\tA\t0.001083\t0.020899\t0.023595\n+949.244445800781\t3\tA\t0.001081\t0.055346\t0.047329\n+914.393310546875\t3\tA\t0.001079\t0.018641\t0.021345\n+923.37158203125\t3\tA\t0.001074\t0.017416\t0.030093\n+967.322998046875\t3\tA\t0.001062\t0.041383\t0.029151\n+961.314880371094\t3\tA\t0.001057\t0.042956\t0.034557\n+994.252197265625\t3\tA\t0.001053\t0.04654\t0.044418\n+945.348083496094\t3\tA\t0.001048\t0.004905\t0.005537\n+913.346313476562\t3\tA\t0.001035\t0.018956\t0.026733\n+914.321105957031\t3\tA\t0.00103\t0.028293\t0.028426\n+929.442138671875\t3\tA\t0.001024\t0.022905\t0.027626\n+922.42822265625\t3\tA\t0.00102\t0.004391\t0.022483\n+978.386474609375\t3\tA\t0.001011\t0.047712\t0.031523\n+939.335510253906\t3\tA\t0.00101\t0.011529\t0.021342\n+929.478515625\t3\tA\t0.00101\t0.037604\t0.039359\n+939.079284667969\t3\tA\t0.001008\t0.03122\t0.044202\n+943.843139648438\t3\tA\t0.000999\t0.02673\t0.036566\n+929.842712402344\t3\tA\t0.000986\t0.083195\t0.108038\n+940.397277832031\t3\tA\t0.000981\t0.015143\t0.027754\n+990.302001953125\t3\tA\t0.000975\t0.039464\t0.035796\n+913.310180664062\t3\tA\t0.000969\t0.010782\t0.026242\n+912.3359375\t3\tA\t0.000967\t0.03343\t0.026227\n+934.327514648438\t3\tA\t0.000965\t0.038056\t0.024783\n+978.34912109375\t3\tA\t0.000952\t0.024638\t0.026361\n+964.427856445312\t3\tA\t0.00095\t0.020628\t0.032363\n+905.135498046875\t3\tA\t0.000939\t0.035836\t0.046276\n+902.9091796875\t3\tA\t0.000928\t0.027048\t0.033126\n+970.296875\t3\tA\t0.000918\t0.041289\t0.037105\n+900.291320800781\t3\tA\t0.000916\t0.036901\t0.029943\n+936.372924804688\t3\tA\t0.000914\t0.03047\t0.017231\n+902.550354003906\t3\tA\t0.000913\t0.020687\t0.031436\n+969.329895019531\t3\tA\t0.000909\t0.03814\t0.02905\n+928.350158691406\t3\tB\t0.000901\t-0.035429\t-0.078124\n+906.465454101562\t3\tA\t0.000895\t0.027815\t0.004156\n+951.195617675781\t3\tA\t0.00089\t0.021378\t0.039051\n+929.296508789062\t3\tA\t0.000889\t0.057417\t0.040791\n+910.389038085938\t3\tA\t0.000889\t0.008833\t0.02408\n+900.362976074219\t3\tA\t0.000884\t0.060121\t0.020862\n+938.274291992188\t3\tA\t0.000883\t0.042087\t0.028046\n+978.423828125\t3\tA\t0.000873\t0.029626\t0.029782\n+911.326171875\t3\tA\t0.000868\t0.039419\t0.029076\n+931.700927734375\t3\tA\t0.000861\t0.028025\t0.033752\n+974.393371582031\t3\tA\t0.000861\t0.041984\t0.028948\n+948.251220703125\t3\tA\t0.000851\t0.058621\t0.045804\n+930.862670898438\t3\tB\t0.000847\t-0.030159\t-0.041363\n+916.923034667969\t3\tA\t0.000845\t0.020133\t0.031831\n+949.318054199219\t3\tA\t0.000845\t0.031551\t0.027948\n+985.459655761719\t3\tA\t0.000843\t0.029168\t0.029559\n+907.4365234375\t3\tA\t0.000843\t0.024964\t0.017428\n+925.18701171875\t3\tA\t0.000838\t0.02295\t0.022881\n+929.332885742188\t3\tB\t0.000837\t-0.029367\t-0.054765\n+937.506225585938\t3\tA\t0.000834\t0.017846\t0.027822\n+987.335083007812\t3\tA\t0.000833\t0.030891\t0.027528\n+987.372619628906\t3\tA\t0.000826\t0.03863\t0.02261\n+991.392211914062\t3\tA\t0.000822\t0.030112\t0.025841\n+986.359619140625\t3\tA\t0.000817\t0.022246\t0.021413\n+995.608337402344\t3\tA\t0.000815\t0.024475\t0.037252\n+901.438415527344\t3\tB\t0.000812\t-0.144815\t-0.105509\n+927.295166015625\t3\tA\t0.00081\t0.03242\t0.019578\n+957.467712402344\t3\tA\t0.000805\t0.034961\t0.029421\n+982.387756347656\t3\tA\t0.000802\t0.029613\t0.024039\n' |
| b |
| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/features_test6.tabular --- a/test-data/features_test6.tabular Thu Oct 25 07:27:54 2018 -0400 +++ b/test-data/features_test6.tabular Fri Feb 15 10:20:01 2019 -0500 |
| b |
| @@ -1,21 +1,21 @@ mz r k s classes centers tstatistics p.values adj.p.values -928.859680175781 2 3 2 B 43.9516959905118 0.541814677313986 0.607464263577403 1 -912.877136230469 2 3 2 B 55.419364071664 0.437808238568372 0.676846169835776 1 -913.887756347656 2 3 2 B 24.9140214890445 0.393340199810185 0.70766449744142 1 -930.862670898438 2 3 2 B 9.28583084091344 0.29858210475084 0.775329712997245 1 -913.923889160156 2 3 2 B 12.1491837287613 0.0960056413112618 0.926642424678888 1 -900.004699707031 2 3 2 A 2.29166666666667 0 1 1 +928.859680175781 2 3 2 B 43.951696 0.541815 0.607464 1 +912.877136230469 2 3 2 B 55.419364 0.437808 0.676846 1 +913.887756347656 2 3 2 B 24.914021 0.39334 0.707664 1 +930.862670898438 2 3 2 B 9.285831 0.298582 0.77533 1 +913.923889160156 2 3 2 B 12.149184 0.096006 0.926642 1 +900.004699707031 2 3 2 A 2.291667 0 1 1 900.04052734375 2 3 2 A 3.125 0 1 1 -900.076354980469 2 3 2 A 3.33333333333333 0 1 1 -900.112182617188 2 3 2 A 3.45833333333333 0 1 1 -900.148010253906 2 3 2 A 3.29166666666667 0 1 1 +900.076354980469 2 3 2 A 3.333333 0 1 1 +900.112182617188 2 3 2 A 3.458333 0 1 1 +900.148010253906 2 3 2 A 3.291667 0 1 1 900.183837890625 2 3 2 A 3.375 0 1 1 -900.219665527344 2 3 2 A 3.66666666666667 0 1 1 -900.255493164062 2 3 2 A 3.91666666666667 0 1 1 -900.291320800781 2 3 2 A 4.08333333333333 0 1 1 -900.3271484375 2 3 2 A 5.79166666666667 0 1 1 -900.362976074219 2 3 2 A 11.5416666666667 0 1 1 -900.398864746094 2 3 2 A 26.2083333333333 0 1 1 -900.434692382812 2 3 2 A 30.0416666666667 0 1 1 -900.470520019531 2 3 2 A 19.1666666666667 0 1 1 +900.219665527344 2 3 2 A 3.666667 0 1 1 +900.255493164062 2 3 2 A 3.916667 0 1 1 +900.291320800781 2 3 2 A 4.083333 0 1 1 +900.3271484375 2 3 2 A 5.791667 0 1 1 +900.362976074219 2 3 2 A 11.541667 0 1 1 +900.398864746094 2 3 2 A 26.208333 0 1 1 +900.434692382812 2 3 2 A 30.041667 0 1 1 +900.470520019531 2 3 2 A 19.166667 0 1 1 900.50634765625 2 3 2 A 8.5 0 1 1 |
| b |
| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/features_test7.tabular --- a/test-data/features_test7.tabular Thu Oct 25 07:27:54 2018 -0400 +++ b/test-data/features_test7.tabular Fri Feb 15 10:20:01 2019 -0500 |
| b |
| b'@@ -1,101 +1,101 @@\n 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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/loadings_pca.tabular --- a/test-data/loadings_pca.tabular Thu Oct 25 07:27:54 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out3.ibd |
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| Binary file test-data/out3.ibd has changed |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out3.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.imzml Fri Feb 15 10:20:01 2019 -0500 |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out3.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.imzml.txt Fri Feb 15 10:20:01 2019 -0500 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 24 +-rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd +-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out4.ibd |
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| Binary file test-data/out4.ibd has changed |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out4.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.imzml Fri Feb 15 10:20:01 2019 -0500 |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out4.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.imzml.txt Fri Feb 15 10:20:01 2019 -0500 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 44 +-rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd +-rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out5.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out5.imzml.txt Fri Feb 15 10:20:01 2019 -0500 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 20 +-rw-r--r-- 1 meli meli 380 Feb 12 00:50 ibd +-rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out6.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out6.imzml Fri Feb 15 10:20:01 2019 -0500 |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/out6.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out6.imzml.txt Fri Feb 15 10:20:01 2019 -0500 |
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| @@ -1,3 +0,0 @@ -mz x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 -329 8.48069807321137 6.00276368862812 0 0 7.22240715797167 6.68463797360356 0 0 0 -345 0 0 4.70593890744759 0 0 0 5.23000350586712 4.17949067812964 5.08555910047608 |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/preprocessing_results4.txt --- a/test-data/preprocessing_results4.txt Thu Oct 25 07:27:54 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,160 +0,0 @@\n-mz\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 3\n-1199\t1.90173968313755\t1.13259535967648\t2.08382650993109\t2.34349737625869\t1.33087314662273\t2.14468085106383\t3.43161925601751\t1.32706902782797\t2.22480967308554\n-1200\t1.39388874502695\t0.970046951574763\t1.52152411836238\t1.35619061126081\t1.10906095551895\t1.66382978723404\t2.22846006564551\t1.19804842790025\t1.7089117778773\n-1201\t1.13095882671438\t0.99102093971692\t1.23623834616944\t1.19344773790952\t1.05864909390445\t1.31063829787234\t1.67396061269147\t1.07824358511023\t1.28168383340797\n-1202\t1.09263589067539\t0.976548887898831\t1.13518929874341\t1.0033640618352\t0.953389126853377\t1.08663829787234\t1.32242888402626\t0.9820310805927\t1.04469323779669\n-1203\t1.10574636879399\t0.91761198121937\t1.07498986623429\t0.954758190327613\t0.902372322899506\t1.05106382978723\t1.17525984682713\t1.05059631369715\t1.11240483654277\n-1204\t1.06972857176487\t0.959559957503684\t1.0088366436968\t1.01262232307474\t0.972948929159802\t1.02127659574468\t1.20315919037199\t0.972262378026744\t1.04388714733542\n-1205\t0.994091198003719\t0.970046951574763\t1.02537494933117\t0.954758190327613\t0.983031301482702\t1.08936170212766\t1.08807439824945\t0.976870256595591\t0.931034482758621\n-1206\t0.886037806916359\t0.970046951574763\t0.955087150385083\t0.972840731811091\t0.947742998352554\t0.94468085106383\t1.05320021881838\t1.00912540657752\t0.959247648902821\n-1207\t1.05171967325031\t0.933342472325988\t1.01297122010539\t0.93305914054744\t0.917495881383855\t0.982978723404255\t1.00786378555799\t0.972262378026744\t0.983430362740708\n-1208\t1.00489653711246\t0.959559957503684\t1.04604783137414\t0.994539781591264\t1.00823723228995\t1.01276595744681\t1.05668763676149\t0.999909649439827\t0.991491267353336\n-1209\t1.34346382918619\t1.15356934781864\t1.26518038102959\t1.31640901999716\t1.0737726523888\t1.20425531914894\t1.19269693654267\t1.23951933501988\t1.12449619346171\n-1210\t1.2413173568116\t1.11749408821413\t1.25029590595865\t1.25333711530279\t1.12277298187809\t1.0743829787234\t1.08472647702407\t1.13685580050596\t1.07564711150918\n-1211\t1.12375526730855\t0.98577744268138\t1.09152817186867\t1.05240391433839\t0.967907742998353\t1.07659574468085\t0.997401531728665\t1.07824358511023\t1.07613076578594\n-1212\t1.05892323265614\t1.04869940710785\t0.979894608836644\t1.00900581477805\t0.993113673805601\t1\t0.979964442013129\t1.04138055655945\t1.06806986117331\n-1213\t0.990489418300808\t0.996264436752459\t1.0088366436968\t1.03432137285491\t1.01831960461285\t0.987234042553191\t0.986939277899344\t1.02294904228406\t1.08419167039857\n-1214\t1.07333035146778\t0.875664004935056\t1.06258613700851\t1.05240391433839\t0.967907742998353\t1.02127659574468\t1.0601750547046\t1.02294904228406\t1.08822212270488\n-1215\t1.15256950493185\t0.964803454539223\t1.11633563032023\t1.07048645582187\t1.0939373970346\t1.17021276595745\t1.13689824945295\t1.08745934224792\t1.205105239588\n-1216\t1.05532145295322\t0.98577744268138\t1.12873935954601\t1.02708835626152\t1.0031960461285\t1.08936170212766\t1.13341083150985\t1.04138055655945\t1.08419167039857\n-1217\t0.950869841568775\t0.975290448610302\t0.959221726793677\t0.961991206921004\t1.02840197693575\t0.970212765957447\t0.955552516411379\t0.972262378026744\t1.01970443349754\n-1218\t0.943666282162951\t0.970046951574763\t0.959221726793677\t0.9656077152177\t0.932619439868204\t0.906382978723404\t0.927653172866521\t1.05981207083484\t1.00761307657859\n-1219\t0.860825348995975\t0.933342472325988\t0.984029185245237\t0.969224223514395\t0.927578253706755\t0.957446808510638\t0.892778993435449\t0.944615106613661\t0.96730855351545\n-1220\t0.929259163351303\t0.938585969361527\t1.00056749087961\t0.889661040987094\t0.962866556836903\t1.00425531914894\t1.07761214442013\t0.986086013733285\t1.08016121809225\n-1221\t0.997692977706632\t0.975290448610302\t0.971625456019457\t0.940292157140831\t0.942701812191104\t1.0936170212766\t1.27290754923414\t1.08745934224792\t1.12449619346171\n-1222\t0.983285858894983\t0.975290448610302\t0.946817997567896\t0.918593107360658\t0.942701812191104\t1.05106382978723\t1.13689824945295\t1.0459884351283\t1.0237348858038'..b'1.02198251523589\n-1333\t1.07113796382253\t1.17089568584911\t1.04407042526568\t1.14721932750828\t1.0625943700308\t1.06123959296947\t1.05168395014746\t1.06261686648544\t1.026188204599\n-1334\t1.0297957967978\t1.08335208316881\t0.923268888458081\t1.08683936290258\t0.98894921567223\t0.981313598519889\t1.03712777090667\t1.0001099919863\t0.950485796063007\n-1335\t0.988453629773075\t0.957508154315864\t0.931897569658624\t0.913246964661195\t0.941605902156006\t0.945790934320074\t0.887926933688517\t0.995301770870979\t0.946280106699897\n-1336\t0.871943886339746\t0.935622253645788\t0.811096032851025\t0.886830730146202\t0.925824797650598\t0.941350601295097\t0.902483112929312\t0.971260665294386\t0.963102864152339\n-1337\t0.860668749878457\t0.979394054985941\t0.836982076452653\t0.943436946964045\t0.978428479335291\t0.914708603145236\t0.851536485586528\t0.937603117487155\t0.90001752370568\n-1338\t0.884073199805679\t1.08111375241846\t0.81188045841471\t0.883743118319774\t0.940410363935899\t0.923791102514507\t0.88643823353889\t0.929953674803693\t1.00248341000692\n-1339\t0.856910371058027\t0.946565203980826\t0.862868120054282\t0.924568208024764\t0.952126638492945\t0.945790934320074\t0.884287888878318\t0.952027780833111\t0.971514242878561\n-1340\t0.920802811005336\t0.935622253645788\t0.793838670449939\t0.909473216873339\t0.994209583840699\t0.959111933395005\t0.906122157739511\t0.865479800757373\t0.992542689694114\n-1341\t0.856910371058027\t0.968451104650903\t0.94915493205971\t0.901925721297627\t0.946866270324475\t0.892506938020352\t0.924317381790505\t0.91837023302588\t0.958897174789229\n-1342\t0.958386599209635\t0.913736352975711\t0.923268888458081\t0.966079433691182\t0.994209583840699\t0.892506938020352\t0.9388735610313\t0.961644223063748\t0.971514242878561\n-1343\t0.856910371058027\t0.962979629483384\t0.893068504256182\t0.939663199176188\t0.973168111166822\t0.932469935245143\t0.866092664827324\t0.923178454141198\t0.984131310967893\n-1344\t0.950869841568775\t0.99033700532098\t0.91895454785781\t0.958531938115469\t0.983688847503761\t0.892506938020352\t0.942512605841499\t0.889520906333967\t0.96730855351545\n-1345\t0.884073199805679\t0.966710180733965\t0.888558057264989\t0.919250654323694\t1.0009045978733\t0.974854932301741\t0.939700616669982\t0.919900121562572\t0.940927411146847\n-1346\t0.879460643980606\t0.946565203980826\t0.94915493205971\t0.920794460236907\t1.00999068834611\t0.905827937095282\t0.913400247359909\t0.985685328640342\t0.929457349247454\n-1347\t0.920802811005336\t0.935622253645788\t0.88875416365591\t0.943436946964045\t0.925824797650598\t0.910268270120259\t0.924317381790505\t0.971260665294386\t0.874783387527016\n-1348\t1.10120499438597\t1.00675143082354\t1.07858515006785\t1.10948184962972\t1.06785473819927\t1.16336725254394\t1.20452383217582\t1.06742508760076\t1.11030199186121\n-1349\t1.10120499438597\t0.984865530153461\t1.10015685306921\t1.10570810184186\t1.08889621087315\t1.06567992599445\t1.17177242888403\t1.13954840433054\t1.13974181740299\n-1350\t1.05610444854081\t1.01769438115858\t0.996612678662695\t0.973626929266894\t0.946866270324475\t0.967992599444958\t1.05532299495766\t1.0770415298314\t1.00936544714656\n-1351\t0.935152984683341\t1.00103125223931\t0.996808785053617\t0.907414808989054\t0.989905646248315\t0.960928433268859\t0.989158543863139\t1.02546243059434\t0.905752554655376\n-1352\t0.898252538082756\t0.962979629483384\t0.975040975661338\t0.947210694751901\t0.994209583840699\t0.910268270120259\t0.862453620017125\t0.956836001948429\t0.870577698163905\n-1353\t0.890735780441896\t0.957508154315864\t0.923268888458081\t0.962305685903325\t0.931085165819067\t0.874745605920444\t0.913400247359909\t0.947219559717792\t0.887400455616348\n-1354\t1.06362120618167\t1.11618093417392\t1.04838476586595\t1.07551811953901\t1.02051142468305\t1.08344125809436\t1.09535248786985\t1.11069907763863\t1.07245078759322\n-1355\t1.17876426640757\t1.01819178799199\t1.08701772487747\t1.1007336161215\t1.0558993559982\t1.09555125725338\t1.09948776606326\t1.05059631369714\t1.03765826649839\n-1356\t1.25341933661339\t1.11461765555463\t1.12696739822804\t1.128350588569\t1.02840197693575\t1.09422492401216\t1.08807439824945\t1.10589085652331\t0.953489859893801\n-1357\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\n' 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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/preprocessing_results5.RData |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/preprocessing_results5.pdf |
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| diff -r 4d5f798a7a18 -r 27a4c660bbca test-data/preprocessing_results5.txt --- a/test-data/preprocessing_results5.txt Thu Oct 25 07:27:54 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,100 +0,0 @@ - x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3 -301 0 0 0 0 0 0 0 0 0 -302 0 4.32197925754431e-23 0 0 0 0 0 0 0 -303 0 1.28620729883923e-30 0 0.00308917369693518 0 0 0 0 0 -304 0 1.32924944261294e-38 0 2.8316210487489e-10 0.411686420440674 0 0 0 0.609295308589935 -305 0 0 0 5.69736818276873e-18 0 0 0.716848015785217 0 0 -306 0 0.180751591920853 0.0924000516533852 3.22355374818131e-26 0.228940084576607 0 0 0 0.338278532028198 -307 5.31794802036641e-23 1.36712752230039e-09 0 0.503042221069336 0.171210870146751 0 0 0.0994685217738152 0.00513129541650414 -308 1.42257959582276e-30 0 0 0 0 0 0 0.0315862037241459 0.322940319776535 -309 1.43981749664202e-38 2.37613022591177e-07 0 0 1.4921518187716e-10 0 7.17280070103395e-32 1.14764100445086e-08 0 -310 0 2.2688041766486e-14 0.0299898684024811 0 4.55189177922775e-18 0 0 2.89623705606364e-14 0 -311 0 4.60080996999485e-22 9.34697319543432e-10 3.53486932303922e-32 5.44664266518465e-26 0 0 6.9618325415624e-22 0 -312 0 0 1.14256191537071e-17 0 0 0 0 6.04272858040201e-30 1.25046502952903e-32 -313 0 0 0 0 0 0 0 0.000948468048591167 0 -314 0 0.343302994966507 0 0 0 0 0 0 0 -315 0 0 0.12950636446476 0 0 0 0 0 0 -316 0.327463179826736 0 1.93941795956221e-09 0.00699668889865279 0 0 0 0.0240590367466211 0 -317 1.18278642435854e-09 0 0 1.591814253743e-07 0 0 0 7.10978553808417e-10 0 -318 0 2.88274619950529e-32 0.312686443328857 1.89643697338752e-14 0 0 0 8.22819137337219e-18 0 -319 0 0 3.68662113032769e-05 3.99332497384422e-22 0 0 0 0 0 -320 0 0 5.68011697044319e-15 2.58921175367487e-30 0 0 0 0 0 -321 0 0 0 0 0 0 0.0821415111422539 0 0 -322 0 0 0 0 0 0 1.23654897432601e-09 8.91581066753133e-07 0 -323 0 0 0 0 0 0 0 3.62019611608189e-14 0 -324 0 0 0 0 0 0 1.41676795295531e-10 5.43261166662179e-22 0 -325 0 0 0 0 0 0 3.87320208074687e-18 0 0 -326 0 0 0 0 0 0 4.08673089735238e-26 0 0.0913732051849365 -327 0.0852032229304314 0 0 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7.14956786396215e-06 0 0 0 2.40733255552072e-09 0 0 -337 0 0 9.22569177086094e-14 0 0 1.92654253432319e-23 0.129606500267982 0 0 -338 0 0 0 0 0 8.21688042580719e-31 0 0 0 -339 0 0 0 0 0 1.2691101966792e-38 0 0 0 -340 0 0 0 0 0.131738051772118 0 0 0 0 -341 0 0 0 0 1.97074911945094e-09 0 2.68033400688056e-31 0 0 -342 0 0 0 0 0 0 0 0 0 -343 0 0.540803730487823 0 0.311067968606949 0 0 0.456998586654663 0 1.1592504051805e-05 -344 0 0.760098695755005 0 1.23029351234436 0.179359897971153 0 0 0 0.385462760925293 -345 1.29758274555206 1.30673027038574 0.626297771930695 0.370624721050262 0.266427725553513 0.95829576253891 0.664171636104584 0.340830773115158 0.920338690280914 -346 0 1.22390151023865 0 0.25139981508255 0 0.280698895454407 0 0 0.700047612190247 -347 0 0.0356887876987457 0 0.208728492259979 0 0 0 0.0668430551886559 0 -348 0 9.81050796156069e-10 5.19627293105376e-24 2.63146238133061e-09 0 0 9.31592096266419e-23 1.41976275180866e-09 0 -349 0 1.04223425420895e-17 6.50702138942878e-31 0 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