From 3d6fa73e909a8f19a4581cba35d1926f25b594ec Mon Sep 17 00:00:00 2001
From: Srimeenakshi Sankaranarayanan <sankaran@hhu.de>
Date: Mon, 2 Sep 2024 12:25:26 +0200
Subject: [PATCH] changed directories and added the quantification files

---
 .gitattributes                                | 1068 ++++++---------
 .../hyphal_polarity_quantification/Readme.txt |    5 +
 .../2805-Ara/Copy of Rotate.tif               |  Bin
 .../2805-Ara/DIC-8.tif                        |    0
 .../2805-glu/Copy of DIC-21.tif               |  Bin
 .../2805-glu/DIC-21.tif                       |    0
 .../2807-Ara/Copy of DIC-13.tif               |  Bin
 .../2807-Ara/DIC-13.tif                       |    0
 .../2807-glu/Copy of Rotate-12.tif            |  Bin
 .../2807-glu/DIC-12.tif                       |    0
 .../8calibrationCopy of Rotate-5.tif          |  Bin
 .../rrm4D-ara/Copy of Rotate-5.tif            |  Bin
 .../rrm4D-ara/DIC-3.tif                       |    0
 .../rrm4D-ara/calibrationCopy of Rotate-5.tif |  Bin
 .../rrm4D_glu/Copy of Rotate.tif              |  Bin
 .../rrm4D_glu/DIC-24.tif                      |    0
 .../wt-ara/Copy of Rotate.tif                 |  Bin
 .../wt-ara/DIC-12.tif                         |    0
 .../wt-glu/Copy of Rotate-3.tif               |  Bin
 .../wt-glu/DIC-21.tif                         |    0
 .../prism_quantification.pzfx                 | 1183 +++++++++++++++++
 .../quantificationcount.xlsx                  |  Bin 0 -> 53420 bytes
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 create mode 100644 assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/Readme.txt
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 rename assays/S2_A2_microscopy_Rrm4-Gfp/dataset/{ => hyphal_polarity_quantification}/microscopy_images_shown_in_manuscript/rrm4D_glu/DIC-24.tif (100%)
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 create mode 100644 assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/prism_quantification.pzfx
 create mode 100644 assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/quantificationcount.xlsx
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diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/Readme.txt b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/Readme.txt
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index 0000000..69b52b3
--- /dev/null
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+2805 - pcr1:rrm4-ada-gfp (ip)
+2807 - pcrg1:rrm4-gfp (ip) 
+Rrm4-Gfp - prrm4: rrm4-Gfp
+A or Ara or on = Arabinose
+G or Gfp or off = Glucose
\ No newline at end of file
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diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/prism_quantification.pzfx b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/prism_quantification.pzfx
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index 0000000..b101055
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+<Constant><Name>Experiment ID</Name><Value/></Constant>
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+<d>wt-glu</d>
+<d>wt-ara</d>
+<d>rrm4D-glu</d>
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+<d>2807-glu</d>
+<d>2807-are</d>
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+<d>3083_ara</d>
+</Subcolumn>
+</RowTitlesColumn>
+<YColumn Width="375" Decimals="5" Subcolumns="3">
+<Title>Unipolar</Title>
+<Subcolumn>
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+<d>21.348</d>
+<d>35.926</d>
+<d>24.044</d>
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+<d>12.717</d>
+<d>22.541</d>
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+	<xsl:template match="ps:Info">
+		<a><xsl:attribute name="name"><xsl:value-of select="@ID"/></xsl:attribute></a>
+		<table border="0">
+			<tr><td><xsl:apply-templates select="ps:Title"/> </td><td width="20"></td><td><b>Notes</b></td></tr>
+			<tr><td valign="top">
+					<table BORDER="1" CELLSPACING="0">
+						<tr><th>Constant</th><th>Name</th></tr>
+						<xsl:for-each select="ps:Constant">
+							<tr>
+								<td><xsl:apply-templates select="ps:Name"/> </td>
+								<td><xsl:apply-templates select="ps:Value"/> </td>
+							</tr>
+						</xsl:for-each>
+					</table>
+				</td>
+				<td width="20">
+				</td>
+				<td valign="top">
+					<xsl:apply-templates select="ps:Notes"/>
+				</td></tr>
+		</table>
+	</xsl:template>
+	<xsl:template match="ps:GraphPadPrismFile">
+		<HTML>
+			<BODY>
+				<xsl:variable name="Chars" select="'ABCDEFGHIJKLMNOPQRSTUVWXYZ'"/>
+				<font color="#999999">
+					<p align="center">This file can be opened by <a href="http://www.graphpad.com">GraphPad</a> Prism (version 
+	<xsl:value-of select="@PrismXMLVersion"/> or later). </p></font><hr/>
+         This file contains <xsl:value-of select="count(ps:Table|ps:HugeTable)"/> data tables and 
+	<xsl:value-of select="count(ps:Info)+count(ps:Table|ps:HugeTable/ps:Info)"/> info tables:
+
+	<dir>
+					<xsl:for-each select="ps:Info">
+						<li>
+							<a>
+								<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
+								<xsl:apply-templates select="ps:Title"/>
+							</a>
+						</li>
+					</xsl:for-each>
+					<xsl:for-each select="ps:Table|ps:HugeTable">
+						<li>
+							<a>
+								<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
+								<xsl:apply-templates select="ps:Title"/>
+							</a>
+							<dir>
+								<xsl:for-each select="ps:Info">
+									<li>
+										<a>
+											<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
+											<xsl:apply-templates select="ps:Title"/>
+										</a>
+									</li>
+								</xsl:for-each>
+							</dir>
+						</li>
+					</xsl:for-each>
+				</dir>
+				<hr/>
+				<xsl:apply-templates select="ps:Info"/>
+				<br/>
+				<hr/>
+				<br/>
+				<xsl:for-each select="ps:Table|ps:HugeTable">
+					<xsl:apply-templates select="ps:Title"/>
+					<a><xsl:attribute name="name"><xsl:value-of select="@ID"/></xsl:attribute></a>
+					<xsl:variable name="width" select="100 div count (*/ps:Subcolumn)"/>
+					<xsl:variable name="xFormat" select="./@XFormat"/>
+					<xsl:variable name="yFormat" select="./@YFormat"/>
+					<xsl:variable name="nRepl" select="./@replicates"/>
+					<xsl:variable name="isXAdvancedColumn" select="boolean(($xFormat='date' or $xFormat='time' or $xFormat='startenddate') and count(ps:XAdvancedColumn) &gt; 0)"/>
+					<xsl:variable name="isXAdvancedSubcol" select="boolean(($xFormat='startenddate') or count(ps:XAdvancedColumn/ps:Subcolumn/ps:Title) &gt; 0)"/>
+					<xsl:variable name="isXSubcol" select="boolean(($xFormat='error' or count(ps:XColumn/ps:Subcolumn/ps:Title) &gt; 0) and not ($isXAdvancedColumn))"/>
+					<xsl:variable name="isYSubcol" select="boolean(($yFormat='replicates'and ./@Replicates&gt;1) or 
+						 ($yFormat!='text'and $yFormat!='replicates') or 
+						count(ps:YColumn/ps:Subcolumn/ps:Title)&gt;0)"/>
+					<xsl:variable name="isYSubColNameCustom" select="boolean($isYSubcol and count(ps:SubColumnTitles)&gt;0)"/>
+					<TABLE BORDER="1" CELLSPACING="0">
+						<TR>
+							<xsl:for-each select="ps:RowTitlesColumn">
+								<TD align="center">
+									<xsl:attribute name="rowspan">
+										<xsl:if test="$isXSubcol or $isXAdvancedSubcol or $isYSubcol">2</xsl:if>
+									</xsl:attribute><BR/>
+								</TD>
+							</xsl:for-each>
+							<xsl:if test="not ($isXAdvancedColumn)">
+								<xsl:for-each select="ps:XColumn">
+									<TD align="center">
+										<xsl:attribute name="rowspan">
+											<xsl:if test="$isYSubcol and not($isXSubcol)">2</xsl:if>
+										</xsl:attribute>
+										<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
+						 
+						<xsl:apply-templates select="ps:Title"/>
+										<xsl:if test="count(ps:Title)=0 or ps:Title=''">X-Title</xsl:if>				
+						 
+					</TD>
+								</xsl:for-each>
+							</xsl:if>
+							<xsl:if test="$isXAdvancedColumn">
+								<xsl:for-each select="ps:XAdvancedColumn">
+									<TD align="center">
+										<xsl:attribute name="rowspan">
+											<xsl:if test="$isYSubcol and not($isXAdvancedSubcol)">2</xsl:if>
+										</xsl:attribute>
+										<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
+						 
+						<xsl:apply-templates select="ps:Title"/>
+										<xsl:if test="count(ps:Title)=0 or ps:Title=''">X-Title</xsl:if>				
+						 
+					</TD>
+								</xsl:for-each>
+							</xsl:if>
+							<xsl:for-each select="ps:YColumn">
+								<xsl:variable name="DefColName2" select="(position()-1) mod 26"/>
+								<xsl:variable name="DefColName1" select="(position()-1-$DefColName2) div 26"/>
+								<TD align="center">
+									<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
+									<xsl:attribute name="rowspan">
+										<xsl:if test="($isXSubcol or $isXAdvancedSubcol) and not($isYSubcol)">2</xsl:if>
+									</xsl:attribute>
+					 
+					<xsl:apply-templates select="ps:Title"/>
+									<xsl:if test="count(ps:Title)=0 or ps:Title=''">
+										<xsl:value-of select="'Data Set-'"/>
+										<xsl:if test="$DefColName1 &gt; 0">
+											<xsl:value-of select="substring($Chars,$DefColName1,1)"/>
+										</xsl:if>
+										<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>
+									</xsl:if>
+					 				
+	   			</TD>
+							</xsl:for-each>
+						</TR>
+						<xsl:if test="$isXSubcol or $isXAdvancedSubcol or $isYSubcol">
+							<TR>
+								<xsl:if test="$isXSubcol">
+									<xsl:for-each select="ps:XColumn">
+										<xsl:for-each select="ps:Subcolumn">
+											<TD align="center"> 
+					 
+					<xsl:apply-templates select="ps:Title"/>
+												<xsl:if test="count(ps:Title)=0 or ps:Title=''">
+													<xsl:choose>
+														<xsl:when test="position()=1"><B>X</B></xsl:when>
+														<xsl:when test="position()=2"><B>Err.Bar</B></xsl:when>
+													</xsl:choose>
+												</xsl:if>				
+					 
+				</TD>
+										</xsl:for-each>
+									</xsl:for-each>
+								</xsl:if>
+								<xsl:if test="$isXAdvancedSubcol">
+									<xsl:for-each select="ps:XAdvancedColumn">
+										<xsl:for-each select="ps:Subcolumn">
+											<TD align="center"> 
+					 
+					<xsl:apply-templates select="ps:Title"/>
+												<xsl:if test="count(ps:Title)=0 or ps:Title=''">
+													<xsl:choose>
+														<xsl:when test="position()=1"><B>Starting Date</B></xsl:when>
+														<xsl:when test="position()=2"><B>Ending Date</B></xsl:when>
+													</xsl:choose>
+												</xsl:if>				
+					 
+				</TD>
+										</xsl:for-each>
+									</xsl:for-each>
+								</xsl:if>
+								<xsl:if test="$isYSubcol">
+									<xsl:for-each select="ps:YColumn">
+										<xsl:variable name="DefColName2" select="(position()-1) mod 26"/>
+										<xsl:variable name="DefColName1" select="(position()-1-$DefColName2) div 26"/>
+										<xsl:variable name="YColumnNdx" select="position()"/>
+										<xsl:for-each select="ps:Subcolumn">
+											<TD align="center">
+					 
+					<xsl:apply-templates select="ps:Title"/>
+												<xsl:if test="count(ps:Title)=0 or ps:Title=''">
+													<xsl:if test="$yFormat='replicates' or $yFormat='text'">
+														<B>
+															<xsl:if test="$DefColName1 &gt; 0">
+																<xsl:value-of select="substring($Chars,$DefColName1,1)"/>
+															</xsl:if>
+															<xsl:choose>
+																<xsl:when test="$isYSubColNameCustom">
+																	<xsl:variable name="subColCustomNamePos" select="position()"/>
+																	<xsl:for-each select="../../ps:SubColumnTitles/ps:Subcolumn">
+																		<xsl:if test="position()=$subColCustomNamePos">
+																			<xsl:choose>
+																				<xsl:when test="../../ps:SubColumnTitles/@OwnSet='1'">
+																					<xsl:variable name="DItemsCount" select="count(./ps:d)"/>
+																					<xsl:choose>
+																						<xsl:when test="$DItemsCount&lt;$YColumnNdx or ./ps:d[$YColumnNdx]=''">
+																							<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
+																						</xsl:when>
+																						<xsl:otherwise>
+																							<xsl:apply-templates select="./ps:d[$YColumnNdx]"/>
+																						</xsl:otherwise>
+																					</xsl:choose>
+																				</xsl:when>
+																				<xsl:when test="../../ps:SubColumnTitles/@OwnSet='0'">
+																					<xsl:variable name="DItemsCount" select="count(./ps:d)"/>
+																					<xsl:choose>
+																						<xsl:when test="$DItemsCount&lt;1 or ./ps:d[1]=''">
+																							<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
+																						</xsl:when>
+																						<xsl:otherwise>
+																							<xsl:apply-templates select="./ps:d[1]"/>
+																						</xsl:otherwise>
+																					</xsl:choose>
+																				</xsl:when>
+																				<xsl:otherwise>
+																					<xsl:apply-templates select="ps:d"/>
+																					<xsl:if test="ps:d=''">
+																						<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
+																					</xsl:if>
+																				</xsl:otherwise>
+																			</xsl:choose>
+																		</xsl:if>
+																	</xsl:for-each>
+																</xsl:when>
+																<xsl:otherwise>
+																	<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
+																</xsl:otherwise>
+															</xsl:choose>
+														</B>
+													</xsl:if>
+													<xsl:if test="$yFormat!='replicates' and $yFormat!='text'">
+														<xsl:if test="not($yFormat='replicates' or $yFormat='text')">
+															<xsl:if test="position()=1"><B>Mean</B></xsl:if>
+															<xsl:if test="position()!=1">
+																<xsl:choose>
+																	<xsl:when test="$yFormat='SD'">
+																		<B>SD</B>
+																	</xsl:when>
+																	<xsl:when test="$yFormat='SE'">
+																		<B>SEM</B>
+																	</xsl:when>
+																	<xsl:when test="$yFormat='CV'">
+																		<B>%CV</B>
+																	</xsl:when>
+																	<xsl:when test="$yFormat='SDN'">
+																		<xsl:if test="position()=2"><B>SD</B></xsl:if>
+																		<xsl:if test="position()=3"><B>N</B></xsl:if>
+																	</xsl:when>
+																	<xsl:when test="$yFormat='SEN'">
+																		<xsl:if test="position()=2"><B>SEM</B></xsl:if>
+																		<xsl:if test="position()=3"><B>N</B></xsl:if>
+																	</xsl:when>
+																	<xsl:when test="$yFormat='CVN'">
+																		<xsl:if test="position()=2"><B>%CV</B></xsl:if>
+																		<xsl:if test="position()=3"><B>N</B></xsl:if>
+																	</xsl:when>
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diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/quantificationcount.xlsx b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/quantificationcount.xlsx
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similarity index 100%
rename from assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-10.tif
rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-10.tif
diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-11.tif b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-11.tif
similarity index 100%
rename from assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-11.tif
rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-11.tif
diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-12.tif b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-12.tif
similarity index 100%
rename from assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-12.tif
rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-12.tif
diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-13.tif b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-13.tif
similarity index 100%
rename from assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-13.tif
rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-13.tif
diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-14.tif b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-14.tif
similarity index 100%
rename from assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-14.tif
rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-14.tif
diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-15.tif b/assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-15.tif
similarity index 100%
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rename to assays/S2_A2_microscopy_Rrm4-Gfp/dataset/hyphal_polarity_quantification/rep1_rrm4_hyper_tribe_quantification/2805/Ara/DIC-15.tif
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