comparison msi_spectra_plots.xml @ 6:2e0368a6bfe8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee

5:4f13aec6d8ff

<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.3">
    <description>
        mass spectrometry imaging mass spectra plots
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
plot(0,type='n',axes=FALSE,ann=FALSE)
#if not $filename:
    #set $filename = $infile.display_name
#end if
title(main=paste0("Plotted mass spectra for file: \n\n","$filename"))


############################# I) numbers ######################################
###############################################################################

    ###########################################################################

    #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
        print("sample pixels")

        ##################### I) Sample: plot full mass spectrum ##############

        ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
        if (!is.null(levels(msidata\$combined_sample))){
            print("combined samples")

                    ## overview plot over combined sample, in case more than 10 combined_samples legend has to be taken from this plot
                    number_combined = length(levels(msidata\$combined_sample))

                    ## the more combined_samples a file has the smaller will be the legend
                    if (number_combined<20){
                        legend_size = 10
                    }else if (number_combined>20 && number_combined<40){
                        legend_size = 9
                    }else if (number_combined>40 && number_combined<60){

                        legend_size = 7
                    }else{
                        legend_size = 6
                    }

                    position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
                    colnames(position_df)[3] = "sample_name"

                    combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
                           geom_tile() +
                           coord_fixed()+
                           ggtitle("Spatial orientation of combined data")+
                           theme_bw()+
                           theme(plot.title = element_text(hjust = 0.5))+
                           theme(text=element_text(family="ArialMT", face="bold", size=12))+
                           theme(legend.position="bottom",legend.direction="vertical")+
                           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
                           guides(fill=guide_legend(ncol=5,byrow=TRUE))
                    coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
                    coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
                    for(file_count in 1:nrow(coord_labels))
                        {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
                        y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}

                    print(combine_plot)

                    ## print legend only for less than 10 samples
                    if (length(levels(msidata\$combined_sample)) < 10){
                        key_legend = TRUE
                    }else{key_legend = FALSE}

            spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero

            plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE)
        }else{
            spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
            plot(msidata, pixel=1:ncol(msidata), key=TRUE)}

        ##################### II) Sample: plot zoom-in mass spectrum ##########

        #if $pixel_conditional.zoomed_sample:

                print("zoomed sample pixels")

                minmasspixel = features(msidata, mz=$token.xlimmin)
                maxmasspixel = features(msidata, mz=$token.xlimmax)

                ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot
                if (!is.null(levels(msidata\$combined_sample))){
                    print("combined samples")
                    plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
                    xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample,
                    key=key_legend,col=hue_pal()(length(levels(msidata\$combined_sample))), superpose=TRUE)
                }else{
                    plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}

            #end for
        #end if

        if (!is.null(levels(msidata\$combined_sample))){
            pixeldf = data.frame(table(msidata\$combined_sample))
        }else{
            pixeldf = data.frame("$filename", ncol(msidata))}
        colnames(pixeldf) = c("sample name", "number of pixels")

    #end if

    ### overview table of pixels or samples:
    plot(0,type='n',axes=FALSE,ann=FALSE)
    title(main="Overview of chosen pixel:")

    ### for more than 20 combined samples print only 20 samples per page:
    if (is.null(levels(msidata\$combined_sample))){
        grid.table(pixeldf, rows= NULL)
    }else if (length(levels(msidata\$combined_sample)) <= 20){
        grid.table(pixeldf, rows= NULL)
    }else{
        grid.table(pixeldf[1:20,], rows= NULL)
        mincount = 21
        maxcount = 40

            </param>
            <when value="single_pixel">
                <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
                    <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
                    <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
                    <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here m/z in Dalton" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
                    <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window in Dalton"/>
                    <param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
                        <option value="white" selected="True">white</option>
                        <option value="black">black</option>
                        <option value="grey">grey</option>
                        <option value="blue">blue</option>

                        <option value="dotted">dotted</option>
                        <option value="longdash">longdash</option>
                    </param>
                    <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
                    <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
                        <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/>
                        <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum m/z for zoomed in window"/>
                    </repeat>
                </repeat>
            </when>
            <when value="sample_pixel">
                <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
                    <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/>
                    <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum m/z for zoomed in window"/>
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>

                <composite_data value="Analyze75.img"/>
                <composite_data value="Analyze75.t2m"/>
            </param>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="sample_pixel"/>
                    <repeat name="zoomed_sample">
                         <param name="xlimmin" value="1250"/>
                         <param name="xlimmax" value="1270"/>
                     </repeat>
            </conditional>
            <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/>
        </test>
        <test>
            <param name="infile" value="123_combined.RData" ftype="rdata"/>

- "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates

    - Enter the x and y coordinates of your pixel of interest
    - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
    - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for the sample/each combined sample

    - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot

Output:

- Pdf with the selected mass spectra plots and additional control plots

6:2e0368a6bfe8

<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.4">
    <description>
        mass spectrometry imaging mass spectra plots
    </description>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>

pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
plot(0,type='n',axes=FALSE,ann=FALSE)
#if not $filename:
    #set $filename = $infile.display_name
#end if
title(main=paste0("Mass spectra for file: \n\n","$filename"))


############################# I) numbers ######################################
###############################################################################

    ###########################################################################

    #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
        print("sample pixels")

        ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)

        #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation':

            ## read and extract x,y,annotation information
            input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE)
            annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)]
            colnames(annotation_input) = c("x", "y", "annotation")

            ## merge with coordinate information of msidata
            msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
            colnames(msidata_coordinates)[3] = "pixel_index"
            merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
            merged_annotation[is.na(merged_annotation)] = "NA"
            merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
            msidata\$annotation = as.factor(merged_annotation[,4])

        #end if

        ##################### I) Sample: plot full mass spectrum ##############

        ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample

        if (!is.null(levels(msidata\$annotation))){
            print("annotated samples")

                    ## overview plot over annotated samples
                    number_combined = length(levels(msidata\$annotation))

                    ## the more annotation groups a file has the smaller will be the legend
                    if (number_combined<20){
                        legend_size = 10
                    }else if (number_combined>20 && number_combined<40){
                        legend_size = 9
                    }else if (number_combined>40 && number_combined<60){

                        legend_size = 7
                    }else{
                        legend_size = 6
                    }

                    position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
                    colnames(position_df)[3] = "sample_name"

                    combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
                           geom_tile() +
                           coord_fixed()+
                           ggtitle("Spatial orientation of annotated data")+
                           theme_bw()+
                           theme(plot.title = element_text(hjust = 0.5))+
                           theme(text=element_text(family="ArialMT", face="bold", size=12))+
                           theme(legend.position="bottom",legend.direction="vertical")+
                           theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
                           guides(fill=guide_legend(ncol=5,byrow=TRUE))

                    print(combine_plot)

                    ## print legend only for less than 10 samples
                    if (length(levels(msidata\$annotation)) < 10){
                        key_legend = TRUE
                    }else{key_legend = FALSE}

            is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
            plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE)
        }else{
            is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
            plot(msidata, pixel=1:ncol(msidata), key=TRUE)}

        ##################### II) Sample: plot zoom-in mass spectrum ##########

        #if $pixel_conditional.zoomed_sample:

                print("zoomed sample pixels")

                minmasspixel = features(msidata, mz=$token.xlimmin)
                maxmasspixel = features(msidata, mz=$token.xlimmax)

                ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot
                if (!is.null(levels(msidata\$annotation))){
                    print("annotation samples")
                    plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),
                    xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation,
                    key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE)
                }else{
                    plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}

            #end for
        #end if

        if (!is.null(levels(msidata\$annotation))){
            pixeldf = data.frame(table(msidata\$annotation))
        }else{
            pixeldf = data.frame("$filename", ncol(msidata))}
        colnames(pixeldf) = c("sample name", "number of pixels")

    #end if

    ### overview table of pixels or samples:
    plot(0,type='n',axes=FALSE,ann=FALSE)
    title(main="Overview of chosen pixel:")

    ### for more than 20 annotation groups print only 20 samples per page:
    if (is.null(levels(msidata\$annotation))){
        grid.table(pixeldf, rows= NULL)
    }else if (length(levels(msidata\$annotation)) <= 20){
        grid.table(pixeldf, rows= NULL)
    }else{
        grid.table(pixeldf[1:20,], rows= NULL)
        mincount = 21
        maxcount = 40

            </param>
            <when value="single_pixel">
                <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
                    <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
                    <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
                    <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
                    <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/>
                    <param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
                        <option value="white" selected="True">white</option>
                        <option value="black">black</option>
                        <option value="grey">grey</option>
                        <option value="blue">blue</option>

                        <option value="dotted">dotted</option>
                        <option value="longdash">longdash</option>
                    </param>
                    <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
                    <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
                        <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
                        <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
                    </repeat>
                </repeat>
            </when>
            <when value="sample_pixel">
            <conditional name="tabular_annotation">
                <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots">
                    <option value="no_annotation" selected="True">pixels belong into one group only</option>
                    <option value="yes_annotation">group pixels according to annotations</option>
                </param>
                    <when value="yes_annotation">
                        <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
                        help="Tabular file with three columns: x values, y values and pixel annotations"/>
                            <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
                            <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
                            <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
                            <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
                    </when>
                    <when value="no_annotation"/>
            </conditional>
                <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
                    <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
                    <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>

                <composite_data value="Analyze75.img"/>
                <composite_data value="Analyze75.t2m"/>
            </param>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="sample_pixel"/>
                <conditional name="tabular_annotation">
                    <param name="load_annotation" value="yes_annotation"/>
                    <param name="annotation_file" value="annotations.tabular" ftype="tabular"/>
                    <param name="column_x" value="1"/>
                    <param name="column_y" value="2"/>
                    <param name="column_names" value="4"/>
                    <param name="tabular_header" value="TRUE"/>
                </conditional>
                <repeat name="zoomed_sample">
                     <param name="xlimmin" value="1250"/>
                     <param name="xlimmax" value="1270"/>
                 </repeat>
            </conditional>
            <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/>
        </test>
        <test>
            <param name="infile" value="123_combined.RData" ftype="rdata"/>

- "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates

    - Enter the x and y coordinates of your pixel of interest
    - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.
    - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot
- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted
    - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot

Output:

- Pdf with the selected mass spectra plots and additional control plots