@@ -453,9 +453,9 @@ line that describes this relationship so we can use it to estimate the
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molecular weights of other proteins in the gel.
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We will use this gel image (@fig-gel ) as an example:
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- [ 26C-10-Coomassie-Blue .jpg] ( data-image/26C-10-Coomassie-Blue .jpg ) . This
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- gel has two sets of results (one each side) -- since only 4 lanes were
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- for each practical group, we put two groups on one gel.
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+ [ sds-page-gel .jpg] ( data-image/sds-page-gel .jpg ) . This gel has two sets
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+ of results (one each side) -- since only 4 lanes were for each practical
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+ group, we put two groups on one gel.
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- Lane 1 (and 10) is the protein ladder which are the proteins of
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known molecular weights.
@@ -478,15 +478,14 @@ the gel image.
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# import gel
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library(imager)
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- gel <- load.image("data-image/26C-10-Coomassie-Blue .jpg")
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+ gel <- load.image("data-image/sds-page-gel .jpg")
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gel_cropped <- crop.borders(gel, nx = 300, ny = 150)
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gel_top <- 180
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gel_bottom <- 990
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pos_patB <- 394
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```
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- : :: {fig-gel}
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-
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+ ::: {fig-gel}
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``` {r}
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#| echo: false
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#| message: false
@@ -526,7 +525,6 @@ be measured from the top of the gel. These distances and the molecular
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weights of the marker proteins are used to create a standard curve that
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allows us to estimate the molecular weight of ShPatB from its position
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on the gel.
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-
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:::
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We will cover two options:
@@ -643,12 +641,12 @@ patB_kda
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You have a file containing the molecular weights of the marker proteins
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[ standard-mw.txt] ( data-image/standard-mw.txt ) and the image of the gel
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- [ 26C-10-Coomassie-Blue .jpg] ( data-image/26C-10-Coomassie-Blue .jpg ) . The
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- molecular weights of the marker proteins are in kilodaltons (kDa)
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+ [ sds-page-gel .jpg] ( data-image/sds-page-gel .jpg ) . The molecular weights
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+ of the marker proteins are in kilodaltons (kDa)
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![ ] ( images/do_in_R.png ) Make a folder call ` data-image ` and save
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[ standard-mw.txt] ( data-image/standard-mw.txt ) and
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- [ 26C-10-Coomassie-Blue .jpg] ( data-image/26C-10-Coomassie-Blue .jpg ) to it
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+ [ sds-page-gel .jpg] ( data-image/sds-page-gel .jpg ) to it
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![ ] ( images/do_in_R.png ) Imort the molecular weights of the marker
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proteins from [ standard-mw.txt] ( data-image/standard-mw.txt )
@@ -666,7 +664,7 @@ library(imager)
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![ ] ( images/do_in_R.png ) Import the gel image:
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``` {r}
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- gel <- load.image("data-image/26C-10-Coomassie-Blue .jpg")
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+ gel <- load.image("data-image/sds-page-gel .jpg")
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```
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Base R's generic ` plot() ` function can handle image files and plot axes
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