changeset 17:611d80c0e29d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0
author galaxyp
date Wed, 19 Apr 2023 22:46:23 +0000
parents 798da6bdff3d
children 83aac7741200
files preprocessing.xml test-data/ComBat_results_Example_processed_file.ibd test-data/ComBat_results_Example_processed_file.imzml test-data/ComBat_results_Example_processed_file.imzml.txt test-data/ComBat_results_Example_processed_file_preprocessing.pdf test-data/Combat_40pixel.ibd test-data/Combat_40pixel.imzML test-data/Example_processed_ComBat_annotation.tabular test-data/annotation_40pixel.tabular test-data/preprocessing_results_combat_40pixel.ibd test-data/preprocessing_results_combat_40pixel.imzml test-data/preprocessing_results_combat_40pixel.imzml.txt test-data/preprocessing_results_combat_40pixel.pdf
diffstat 13 files changed, 3068 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/preprocessing.xml	Tue Feb 22 20:56:10 2022 +0000
+++ b/preprocessing.xml	Wed Apr 19 22:46:23 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
     <description>
         mass spectrometry imaging preprocessing
     </description>
@@ -7,7 +7,9 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <requirement type="package" version="3.4.0">r-ggplot2</requirement>
+        <requirement type="package" version="3.40.0">bioconductor-sva</requirement>
+        <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -41,6 +43,8 @@
 library(Cardinal)
 library(gridExtra)
 library(ggplot2)
+library(sva)
+library(randomcoloR)
 
 
 @READING_MSIDATA_FULLY_COMPATIBLE@
@@ -448,6 +452,120 @@
             print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after transformation", outer=TRUE, line=0)
 
+
+            
+            
+        ############################### ComBat batch correction ###########################
+
+        #elif str( $method.methods_conditional.preprocessing_method) == 'ComBat_batch_correction':
+            print('ComBat batch correction of centroided data')
+
+            ## load annotation tabular and define batch and condition column
+            annotation = read.delim("$method.methods_conditional.annotation_file", header=$method.methods_conditional.feature_header, sep="\t")
+            annotation_x = annotation[,$method.methods_conditional.x_column]
+            annotation_y = annotation[,$method.methods_conditional.y_column]
+            batch = annotation[,$method.methods_conditional.batch_column]
+            condition = annotation[,$method.methods_conditional.condition_column]
+            
+            ### stop if not enough batches provided
+                tryCatch(
+                        {
+
+                        if (unique(batch<2))
+                            {
+                            stop(call.=FALSE)
+                            }
+                        },
+                        error=function(cond) {
+                        ## in case user provided an annotation tabular with less than two batches
+                            message("Error in annotation tabular")
+                            message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary)")
+                            stop(call.=FALSE)
+                        }
+                    )
+            
+            ## get intensity matrix from imzml file
+            intensity_matrix = as.matrix(iData(msidata))
+            mz_names = paste0("mz_", mz(msidata))
+            pixel_names = paste0("xy_", msidata@elementMetadata@coord@listData[["x"]], "_", msidata@elementMetadata@coord@listData[["y"]])
+            rownames(intensity_matrix) = mz_names
+            colnames(intensity_matrix) = pixel_names
+
+            ## reorder columns of intensity matrix to row order of batch column
+            rownames(annotation) = paste0("xy_", annotation_x, "_", annotation_y)
+            col_order = rownames(annotation)
+            
+            ### stop if pixel/sample names (columns) in intensity matrix from imzml file don't match samples names (rows) in annotation tabular file            
+            	tryCatch(
+                        {
+
+                        if (all(colnames(intensity_matrix) %in% col_order == FALSE))
+                            {
+                            stop(call.=FALSE)
+                            }
+                        },
+                        error=function(cond) {
+                        ## in case pixel names (columns) from the imzml file don't match the pixel names in the annotation tabular file
+                            message("Error in annotation tabular")
+                            message("Possible problems: Annotation tabular file does not contain the correct pixel names (columns) from the imzml file)")
+                            stop(call.=FALSE)
+                        }
+                    )      
+            
+            intensity_matrix = intensity_matrix[, col_order]
+            print("columns have been ordered to annotation row order")
+
+            ## execution of ComBat algorithm from sva package
+            combat_data = ComBat(dat = intensity_matrix, batch = batch, mod = NULL, par.prior = TRUE, prior.plots = FALSE)
+            print("Combat has been executed")
+
+            ## change intensity data of loaded imzml file after combat has been performed
+            iData(msidata) = as.matrix(combat_data)   
+            
+            ############################### QC ###########################
+            
+            maxfeatures =nrow(msidata)
+            pixelcount = ncol(msidata)
+            minmz = round(min(mz(msidata)), digits=2)
+            maxmz = round(max(mz(msidata)), digits=2)
+            batch_corrected = c(minmz, maxmz, maxfeatures, pixelcount)
+            QC_numbers= cbind(QC_numbers, batch_corrected)
+            vectorofactions = append(vectorofactions, "batch_corrected")
+            print(plot(msidata, pixel=random_spectra, col="black"))
+            title("Spectra after ComBat batch correction", outer=TRUE, line=0)
+
+
+            ## PCA plot function and execution
+	    combat_data = as.data.frame(combat_data)
+	    intensity_data = as.data.frame(intensity_matrix)
+
+	    ## PCA function
+            plot_PCA = function(input_data, condition, batch, title, color){
+                data <- input_data
+                pca_data <- prcomp(t(data[, seq_len(ncol(input_data))]))
+                pca_sdev <- pca_data[["sdev"]]
+                pca_data_perc <- round(100 * pca_sdev^2 / sum(pca_sdev^2), 1)
+                pca_components <- pca_data[["x"]]
+                df_pca_data <- data.frame(PC1 = pca_components[, 1], PC2 = pca_components[, 2], sample = colnames(input_data), condition = condition)
+                ggplot(df_pca_data, aes(PC1, PC2, color = as.factor(batch), shape = as.factor(condition))) +
+                ggtitle(title) +
+                geom_point(size = 4) +
+                stat_ellipse(aes(PC1, PC2, color = as.factor(batch), group = as.factor(batch)), type = "norm")+
+                scale_color_manual(values=color) +
+                theme_bw() +
+                theme(legend.position = "bottom", legend.box="vertical", plot.title = element_text(size = 12, hjust = 0.5), axis.title = element_text(size = 12), axis.text = element_text(size = 12, color = "black")) +
+                labs(x=paste0("PC1 (",pca_data_perc[1],")"), y=paste0("PC2 (",pca_data_perc[2],")")) +
+                labs(color = "Batches", shape = "Conditions")}
+
+	    ## define colors
+	    color_pal = distinctColorPalette(length(levels(as.factor(batch))))
+
+            ## execution of PCA plots
+            PCA_bc = plot_PCA(intensity_data, condition, batch, "before batch correction", color_pal)
+            PCA_ac = plot_PCA(combat_data, condition, batch, "batch corrected", color_pal)
+            print(PCA_bc)
+            print(PCA_ac)
+            
             #end if
     #end for
 
@@ -492,6 +610,7 @@
                     <option value="Peak_binning">Peak binning to reference peaks</option>
                     <option value="Mass_binning">m/z binning</option>
                     <option value="Transformation">Transformation</option>
+                    <option value="ComBat_batch_correction">ComBat batch correction of centroided data</option>
                 </param>
                 <when value="Normalization">
                     <conditional name="methods_for_normalization">
@@ -690,6 +809,14 @@
                             <when value="sqrt"/>
                     </conditional>
                 </when>
+                <when value="ComBat_batch_correction">
+		     <param name="annotation_file" type="data" format="tabular" label="Annotation file that contains the pixel x and y coordinates, the batch identifier, and the condition annotation for each spectrum." help="Annotation tabular file that contains the batch identifier for each spectrum in one column."/>
+                       <param name="x_column" type="data_column" data_ref="annotation_file" label="X coordinates" help="Column with x coordinates of pixels."/>
+                       <param name="y_column" type="data_column" data_ref="annotation_file" label="Y coordinates" help="Column with y ccordinates of pixels."/>
+                       <param name="batch_column" type="data_column" data_ref="annotation_file" label="Batch column" help="The column that contains the batch identifier for each spectrum."/>
+                       <param name="condition_column" type="data_column" data_ref="annotation_file" label="Condition column" help="The column that contains the condition annotation for each spectrum. Typically these are the groups you want to compare. If not applicable, the batch column can be selected again as this information is only used for the QC plot."/>
+                       <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
+                </when>
             </conditional>
         </repeat>
     </inputs>
@@ -870,6 +997,52 @@
                 <extra_files type="file" file="preprocessing_results5.ibd" name="ibd" compare="sim_size"/>
             </output>
         </test>
+        <test>
+            <param name="infile" value="" ftype="imzml">
+                <composite_data value="Combat_40pixel.imzML" />
+                <composite_data value="Combat_40pixel.ibd"/>
+            </param>
+            <repeat name="methods">
+                <conditional name="methods_conditional">
+                    <param name="preprocessing_method" value="ComBat_batch_correction"/>
+                    <param name="annotation_file" value="annotation_40pixel.tabular" ftype="tabular"/>
+                    <param name="feature_header" value="TRUE"/>
+                    <param name="x_column" value="2"/>
+                    <param name="y_column" value="3"/>
+                    <param name="batch_column" value="4"/>
+                    <param name="condition_column" value="6"/>
+                </conditional>
+            </repeat>
+            <output name="QC_overview" file="preprocessing_results_combat_40pixel.pdf" compare="sim_size"/>
+            <output name="outfile_imzml" ftype="imzml" file="preprocessing_results_combat_40pixel.imzml.txt" compare="sim_size">
+                <extra_files type="file" file="preprocessing_results_combat_40pixel.imzml" name="imzml" lines_diff="6"/>
+                <extra_files type="file" file="preprocessing_results_combat_40pixel.ibd" name="ibd" compare="sim_size"/>
+            </output>
+        </test>
+        <test>
+            <expand macro="processed_infile_imzml"/>
+            <conditional name="processed_cond">
+                <param name="processed_file" value="processed"/>
+                <param name="accuracy" value="50"/>
+                <param name="units" value="ppm"/>
+            </conditional>
+            <repeat name="methods">   
+                <conditional name="methods_conditional">
+                    <param name="preprocessing_method" value="ComBat_batch_correction"/>
+                    <param name="annotation_file" value="Example_processed_ComBat_annotation.tabular" ftype="tabular"/>
+                    <param name="feature_header" value="TRUE"/>
+                    <param name="x_column" value="2"/>
+                    <param name="y_column" value="3"/>
+                    <param name="batch_column" value="4"/>
+                    <param name="condition_column" value="5"/>
+                </conditional>
+            </repeat>
+            <output name="QC_overview" file="ComBat_results_Example_processed_file_preprocessing.pdf" compare="sim_size"/>
+            <output name="outfile_imzml" ftype="imzml" file="ComBat_results_Example_processed_file.imzml.txt" compare="sim_size">
+                <extra_files type="file" file="ComBat_results_Example_processed_file.imzml" name="imzml" lines_diff="6"/>
+                <extra_files type="file" file="ComBat_results_Example_processed_file.ibd" name="ibd" compare="sim_size"/>
+            </output>
+        </test>
     </tests>
     <help>
         <![CDATA[
@@ -896,6 +1069,20 @@
 - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
 - m/z binning: generates new m/z bins
 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 
+- ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:
+ 
+ ::
+ 
+   	   x_coord     y_coord      batch_identifier	condition
+  	       10          29          TMA_1                  A
+  	       22          14          TMA_1                  B
+  	       22          27          TMA_2                  A
+  	       23           7          TMA_2                  B
+   	       29          45          TMA_3                  A
+   	       33          41          TMA_3                  B
+   	    ...
+   	    ...
+
                     
 
 **Output**
Binary file test-data/ComBat_results_Example_processed_file.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ComBat_results_Example_processed_file.imzml	Wed Apr 19 22:46:23 2023 +0000
@@ -0,0 +1,340 @@
+<?xml version="1.0"?>
+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+	<cvList count="3">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
+		<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
+		<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="82e7db90-df72-41f8-9ca7-7a19e966d5c1" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="259aa4b90129abb2f1f3107cf123f28d7c744f0c" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
+		</fileContent>
+	</fileDescription>
+	<referenceableParamGroupList count="4">
+		<referenceableParamGroup id="spectrum1">
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="mzArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="intensityArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
+		</referenceableParamGroup>
+	</referenceableParamGroupList>
+	<sampleList count="1">
+		<sample id="sample1" name="Sample1">
+			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
+		</sample>
+	</sampleList>
+	<softwareList count="1">
+		<software id="Cardinal" version="2.10.0">
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<scanSettingsList count="1">
+		<scanSettings id="scansettings1">
+			<cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+			<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
+		</scanSettings>
+	</scanSettingsList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="IC1">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="CardinalWriteImzML">
+			<processingMethod order="1" softwareRef="Cardinal">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
+		<spectrumList count="9" defaultDataProcessingRef="CardinalWriteImzML">
+			<spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+						<userParam name="3DPositionX" value="1.000000" />
+						<userParam name="3DPositionY" value="1.000000" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="166372" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+						<userParam name="3DPositionX" value="2.000000" />
+						<userParam name="3DPositionY" value="1.000000" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="332728" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+						<userParam name="3DPositionX" value="3.000000" />
+						<userParam name="3DPositionY" value="1.000000" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="499084" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ComBat_results_Example_processed_file.imzml.txt	Wed Apr 19 22:46:23 2023 +0000
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+imzML file:
+total 1648
+-rw-r--r-- 1 ubuntu ubuntu 1663576 Feb 15 11:25 ibd
+-rw-r--r-- 1 ubuntu ubuntu   18593 Feb 15 11:25 imzml
Binary file test-data/ComBat_results_Example_processed_file_preprocessing.pdf has changed
Binary file test-data/Combat_40pixel.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Combat_40pixel.imzML	Wed Apr 19 22:46:23 2023 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_processed_ComBat_annotation.tabular	Wed Apr 19 22:46:23 2023 +0000
@@ -0,0 +1,10 @@
+spectra_names	x_values	y_values	batch_id	condition
+xy_1_1	1	1	B_1	A
+xy_2_1	2	1	B_1	B
+xy_3_1	3	1	B_1	A
+xy_1_2	1	2	B_1	B
+xy_2_2	2	2	B_2	A
+xy_3_2	3	2	B_2	B
+xy_1_3	1	3	B_2	A
+xy_2_3	2	3	B_2	B
+xy_3_3	3	3	B_2	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation_40pixel.tabular	Wed Apr 19 22:46:23 2023 +0000
@@ -0,0 +1,41 @@
+xy_x_y	x	y	TMA_Batch	Sample	Tissue
+xy_10_29	10	29	TMA_397	TMA_397_C-2_Tumor	Tumor
+xy_22_14	22	14	TMA_402	TMA_402_C-3_Stroma	Stroma
+xy_22_27	22	27	TMA_394	TMA_394_A-1_Stroma	Stroma
+xy_23_7	23	7	TMA_402	TMA_402_C-3_Stroma	Stroma
+xy_24_26	24	26	TMA_394	TMA_394_A-1_Stroma	Stroma
+xy_24_6	24	6	TMA_402	TMA_402_C-3_Stroma	Stroma
+xy_29_45	29	45	TMA_394	TMA_394_A-1_Tumor	Tumor
+xy_2_10	2	10	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_33_41	33	41	TMA_394	TMA_394_A-1_Tumor	Tumor
+xy_34_43	34	43	TMA_394	TMA_394_A-1_Tumor	Tumor
+xy_34_5	34	5	TMA_400	TMA_400_A-4_Tumor	Tumor
+xy_36_3	36	3	TMA_400	TMA_400_A-4_Tumor	Tumor
+xy_38_3	38	3	TMA_400	TMA_400_A-4_Tumor	Tumor
+xy_3_4	3	4	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_48_5	48	5	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_49_11	49	11	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_49_9	49	9	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_51_6	51	6	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_52_8	52	8	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_53_11	53	11	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_53_14	53	14	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_55_8	55	8	TMA_400	TMA_400_A-4_Stroma	Stroma
+xy_5_24	5	24	TMA_397	TMA_397_C-2_Tumor	Tumor
+xy_5_5	5	5	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_62_6	62	6	TMA_398	TMA_398_E-2_Tumor	Tumor
+xy_64_9	64	9	TMA_398	TMA_398_E-2_Tumor	Tumor
+xy_6_3	6	3	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_6_4	6	4	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_6_5	6	5	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_6_7	6	7	TMA_402	TMA_402_C-3_Tumor	Tumor
+xy_71_8	71	8	TMA_398	TMA_398_E-2_Stroma	Stroma
+xy_73_6	73	6	TMA_398	TMA_398_E-2_Stroma	Stroma
+xy_73_7	73	7	TMA_398	TMA_398_E-2_Stroma	Stroma
+xy_74_7	74	7	TMA_398	TMA_398_E-2_Stroma	Stroma
+xy_7_53	7	53	TMA_397	TMA_397_C-2_Stroma	Stroma
+xy_8_55	8	55	TMA_397	TMA_397_C-2_Stroma	Stroma
+xy_8_56	8	56	TMA_397	TMA_397_C-2_Stroma	Stroma
+xy_9_52	9	52	TMA_397	TMA_397_C-2_Stroma	Stroma
+xy_9_53	9	53	TMA_397	TMA_397_C-2_Stroma	Stroma
+xy_9_56	9	56	TMA_397	TMA_397_C-2_Stroma	Stroma
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+++ b/test-data/preprocessing_results_combat_40pixel.imzml	Wed Apr 19 22:46:23 2023 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results_combat_40pixel.imzml.txt	Wed Apr 19 22:46:23 2023 +0000
@@ -0,0 +1,4 @@
+imzML file:
+total 132
+-rw-r--r-- 1 ubuntu ubuntu 63648 Feb  7 17:01 ibd
+-rw-r--r-- 1 ubuntu ubuntu 66384 Feb  7 17:01 imzml
Binary file test-data/preprocessing_results_combat_40pixel.pdf has changed