|
19 | 19 | "tags": [] |
20 | 20 | }, |
21 | 21 | "source": [ |
22 | | - "In this tutorial we will look at a colorectal cancer (CRC) sample profiled using VisiumHD. The data is available from the 10X website (see [here](https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc)).\n", |
| 22 | + "In this tutorial, we will look at a colorectal cancer (CRC) sample profiled using VisiumHD. The data is available from the 10x Genomics website (see [here](https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc)).\n", |
23 | 23 | "\n", |
24 | | - "To follow along you will need to download the data and install some additional packages;\n", |
| 24 | + "To follow along, you will need to download the data and install some additional packages;\n", |
25 | 25 | "`scanpy` and `spatialdata_io`." |
26 | 26 | ] |
27 | 27 | }, |
|
116 | 116 | "tags": [] |
117 | 117 | }, |
118 | 118 | "source": [ |
119 | | - "First we will generate cell type signature based on the 16 µm bins VisiumHD. Theoretically this should also work when using the 8 µm bins or segmentation-based cells. The signatures are then later used to map the cell types to the original 2 µm resolution.\n", |
| 119 | + "First, we will generate cell-type signatures based on the 16 µm bins in VisiumHD.\n", |
| 120 | + "Theoretically, this should also work when using the 8 µm bins or segmentation-based cells.\n", |
| 121 | + "The signatures are then later used to map the cell types to the original 2 µm resolution.\n", |
120 | 122 | "\n", |
121 | | - "This whole section can be replaced by your favorite single-cell workflow. We will follow a simple workflow here as this is not the main purpose of this tutorial." |
| 123 | + "This whole section can be replaced by your favorite single-cell workflow. We will follow a simple workflow here, as this is not the main purpose of this tutorial." |
122 | 124 | ] |
123 | 125 | }, |
124 | 126 | { |
|
230 | 232 | "tags": [] |
231 | 233 | }, |
232 | 234 | "source": [ |
233 | | - "Now we apply our favorite workflow to find clusters/cell types. Remember that you can adjust the processing here to your liking! For example you could switch to spatially variable genes instead of highly variable." |
| 235 | + "Now we apply our favorite workflow to find clusters/cell types.\n", |
| 236 | + "Remember that you can adjust the processing here to your liking!\n", |
| 237 | + "For example, you could switch to spatially variable genes instead of highly variable." |
234 | 238 | ] |
235 | 239 | }, |
236 | 240 | { |
|
352 | 356 | "source": [ |
353 | 357 | "Now we are ready to generate the cell type signatures.\n", |
354 | 358 | "\n", |
355 | | - "The only thing to keep in mind if you don't follow the workflow above is that the signatures should be non-negative i.e. they should not be generated from z-scores or Pearson residuals, etc. which does not mean that you can't use these methods to do the cell typing just make sure to use the log-transformed counts to calculate the signatures.\n", |
| 359 | + "The only thing to keep in mind if you don't follow the workflow above is that the signatures should be non-negative, i.e., they should not be generated from z-scores or Pearson residuals, etc.\n", |
| 360 | + "This does not mean that you can't use these methods to do the cell typing.\n", |
| 361 | + "Just make sure to use the log-transformed counts to calculate the signatures.\n", |
356 | 362 | "\n", |
357 | 363 | "Here, we will only use the highly variable genes." |
358 | 364 | ] |
|
609 | 615 | "tags": [] |
610 | 616 | }, |
611 | 617 | "source": [ |
612 | | - "To compare the cell typing we will plot the unbinned and binned data next to each other.\n", |
| 618 | + "To compare the cell typing, we will plot the unbinned and binned data next to each other.\n", |
613 | 619 | "\n", |
614 | | - "First lets get the images for the cell typing of the unbinned data. " |
| 620 | + "First, let's get the images for the cell typing of the unbinned data. " |
615 | 621 | ] |
616 | 622 | }, |
617 | 623 | { |
|
692 | 698 | "tags": [] |
693 | 699 | }, |
694 | 700 | "source": [ |
695 | | - "Now we are ready to compare the results. We will also include the KDE as it gives us an orientation of what the tissue looks like. " |
| 701 | + "Now we are ready to compare the results.\n", |
| 702 | + "We will also include the KDE, as it gives us an orientation of what the tissue looks like. " |
696 | 703 | ] |
697 | 704 | }, |
698 | 705 | { |
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