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Commit 8936c796 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tutorial: clonotypes (at some places)

We now keep 'clones' all along the tutorial, except when describing elements of the interface.
parent e22da76e
......@@ -30,14 +30,14 @@ is \texttt{IGHV3-9 7/CCCGGA/17 J6*02}.
assert ( cinfo[:name].text == "IGHV3-9 7/CCCGGA/17 J6*02"), "correct name for first clone"
stats = $b.statsline
assert (stats.text.include? '1 clone, 189 991 reads (9.665%)'), "Correct stats, number of reads and percentage"
assert (stats.text.include? '1 clonotype, 189 991 reads (9.665%)'), "Correct stats, number of reads and percentage: " + stats.text
end
\end{verbatim}
There are several options to display the V(D)J designation.
\question{In the \com{settings} menu, under \com{N regions in clone names} select \com{length} to show N zones by their length. Revert to the
\question{In the \com{settings} menu, under \com{N regions in clonotype names} select \com{length} to show N zones by their length. Revert to the
default \com{sequence (when short)} setting to show the full N on short sequences.}
\begin{verbatim}
......@@ -73,7 +73,7 @@ There are several options to display the V(D)J designation.
end
\end{verbatim}
\question{Try also the options \com{alleles in clone names} : by selecting \com{always}, the clone
\question{Try also the options \com{alleles in clonotype names} : by selecting \com{always}, the clone
V gene is displayed as \com{IGHV3-9*01}. Revert to the default \com{when not
*01}. This setting, which is the default, allows to have a more condensed
V(D)J designation that doesn't make the \com{*01} appear (it is implicit).}
......@@ -85,7 +85,7 @@ There are several options to display the V(D)J designation.
$b.input(:id => "menuAlleleNot_never").click
$b.update_icon.wait_while(&:present?) # wait update
cinfo = $b.clone_info("1")
assert ( cinfo[:name].text == "IGHV3-9 7/6/17 J6"), "correct name for first clone (menuAlleleNot_never)"
assert ( cinfo[:name].text == "IGHV3-9 7/6/17 J6"), "correct name for first clone (menuAlleleNot_never): " + cinfo[:name].text
$b.menu_settings.click
$b.input(:id => "menuAlleleNot_when_not_01").click
......@@ -110,11 +110,11 @@ depending if the top 50 are always the same or always different or, more
realistically, in-between.
This number can be increased to a maximum of 100 clones by going to the \com{filter} menu and by putting the
slider to its right end.
\question{Notice how the IGH smaller clones percentage (second clone displayed in the list) changes. What was its
\question{Notice how the IGH smaller clonotypes percentage (second clone displayed in the list) changes. What was its
initial value? What is it now?}
\reponse{filter set to 50 \fl IGH smaller clones 10.11\,\%\\*
filter set to 100 \fl IGH smaller clones 8.92\,\%\\*}
\reponse{filter set to 50 \fl IGH smaller clonotypes 10.11\,\%\\*
filter set to 100 \fl IGH smaller clonotypes 8.92\,\%\\*}
\begin{verbatim}
def test_B_clones_04_filter_slider
if not ENV['HEADLESS']
......@@ -153,7 +153,7 @@ slider to its right end.
end
\end{verbatim}
The \textit{smaller clones} correspond to clones that are not displayed
The \textit{smaller clonotypes} correspond to clones that are not displayed
because they are never among the most abundant ones.
......@@ -161,7 +161,7 @@ because they are never among the most abundant ones.
Consider the most abundant clones in the list: \texttt{IGHV3-9 7/CCCGGA/17 J6*02} and \texttt{TRGV10 13//5 JP1}.
Usually we may want to tag them in order to remember them later on.
\question{Click on the star and choose colored tags for these two clones, such as \texttt{clone 1} or \texttt{clone 2}.
\question{Click on the star and choose colored tags for these two clones, such as \texttt{clonotype 1} or \texttt{clonotype 2}.
Notice how the color applies throughout all the views.}
\begin{verbatim}
......@@ -194,11 +194,11 @@ Later you may want to filter clones depending on the tags you have chosen.
assert ($b.clone_in_list("1").present?), "clone 0 is present at starting test"
# Click on tag switch; clone 1 will be hidden
$b.info_colorBy.span(title: 'clone 1').click
$b.info_colorBy.span(title: 'clonotype 1').click
$b.update_icon.wait_while(&:present?)
assert (not $b.clone_in_list("1").present?), "clone 0 is hidden"
$b.info_colorBy.span(title: 'clone 1').click
$b.info_colorBy.span(title: 'clonotype 1').click
$b.update_icon.wait_while(&:present?)
assert ($b.clone_in_list("1").present?), "clone 0 is present at the end of the test"
end
......@@ -864,8 +864,8 @@ be similar.
end
\end{verbatim}
\question{ Instead of coloring by clone's size, you could also color by
\com{clone}. When coloring by \com{clone}, each clone has a random color. Thus in
\question{ Instead of coloring by clone size, you could also color by
\com{clonotype}. When coloring by \com{clonotype}, each clone has a random color. Thus in
a bar plot, it is a convenient color mode to see the peaks that are due to a
single clone or to several clones.
However clones may be very similar. Another option is to color by
......@@ -875,7 +875,7 @@ be similar.
\begin{verbatim}
def test_B_clones_32_color_by_clone
select_color = $b.select_list(:id => "color_menu_select")
select_color.select("Clone")
select_color.select("Clonotype")
$b.update_icon.wait_while(&:present?)
$b.clone_in_list("0").click
......
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