Upload dendrogram + PCA clustering script #4
Conversation
ghost
requested a review
from 
| python3 tcga_fpkm_dendrogram.py <filename> | ||
| ``` | ||
|
|
||
| A folder called `results` will be created which will contain the following output files: |
There was a problem hiding this comment.
Can you list the generated output files and give a brief description of them here?
| @@ -0,0 +1,53 @@ | |||
| # TCGA_FPKM_dendrogram | |||
There was a problem hiding this comment.
In general, we want this script to be a generic dendogram + PCA clustering script, not necessarily focused on the TCGA data set. So it's best not to mention TCGA in the documentation or in the code.
| Once you have activated the `virtualenv`, use the script as follows: | ||
|
|
||
| ```bash | ||
| python3 tcga_fpkm_dendrogram.py <filename> |
There was a problem hiding this comment.
Can you add a brief description of the how the input file should look like? Maybe a small example as well?
| def plot_dendro_interactive(data, labels): | ||
| data_array = tcga_data.to_numpy() | ||
| fig = ff.create_dendrogram(data_array, orientation='left', labels=labels) | ||
| fig.update_layout(width=1600, height=800) | ||
| fig.write_image('./results/TCGA-FPKM_dendrogram-intr.png') | ||
| fig.show() |
There was a problem hiding this comment.
Might as well remove this function since it's no longer used.
| @@ -0,0 +1,96 @@ | |||
| from sklearn.cluster import AgglomerativeClustering | |||
There was a problem hiding this comment.
Remember to remove all mentions of TCGA.
| sys.exit() | ||
|
|
||
| # Create directory for results | ||
| path = './results' |
There was a problem hiding this comment.
Can you add a parameter for the user to specify the name of the output directory?
fabubaker
changed the title
2 participants
No description provided.