Mercurial > repos > goeckslab > scimap_plotting
changeset 2:ef73596d678a draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
| author | goeckslab |
|---|---|
| date | Tue, 30 Jul 2024 18:20:43 +0000 |
| parents | c42e97dc5a3a |
| children | |
| files | main_macros.xml scimap_plotting.py scimap_plotting.xml |
| diffstat | 3 files changed, 23 insertions(+), 23 deletions(-) [+] |
line wrap: on
line diff
--- a/main_macros.xml Wed Jun 26 15:26:55 2024 +0000 +++ b/main_macros.xml Tue Jul 30 18:20:43 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.1.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">20.01</token> <xml name="scimap_requirements">
--- a/scimap_plotting.py Wed Jun 26 15:26:55 2024 +0000 +++ b/scimap_plotting.py Tue Jul 30 18:20:43 2024 +0000 @@ -3,7 +3,7 @@ import os import warnings -import matplotlib.pylab as plt +import matplotlib.pyplot as plt import numpy as np import scimap as sm import seaborn as sns @@ -37,9 +37,11 @@ # parse list text arguments for o in options.copy(): - opt_list = options.pop(o) - if opt_list: - options[o] = [x.strip() for x in opt_list.split(',')] + opt = options.pop(o) + if o == 'matplotlib_cmap': + matplotlib_cmap = opt + elif opt != "": + options[o] = [x.strip() for x in opt.split(',')] # add base args into options dict to pass to tool options['x_axis'] = params['analyses']['x_axis'] @@ -50,15 +52,6 @@ df = sm.pl.stacked_barplot(adata, **options) - # Pick cmap to use - num_phenotypes = len(df.columns) - 1 - if num_phenotypes <= 9: - matplotlib_cmap = "Set1" - elif num_phenotypes > 9 and num_phenotypes <= 20: - matplotlib_cmap = plt.cm.tab20 - else: - matplotlib_cmap = plt.cm.gist_ncar - # Plotting sns.set_theme(style="white") ax = df.plot.bar(stacked=True, cmap=matplotlib_cmap)
--- a/scimap_plotting.xml Wed Jun 26 15:26:55 2024 +0000 +++ b/scimap_plotting.xml Tue Jul 30 18:20:43 2024 +0000 @@ -38,6 +38,20 @@ <param argument="subset_yaxis" type="text" value="" optional="true" label="Subset y-axis prior to plotting. Type in a list of categories to include on y-axis" help="Optional. Comma delimited. Default is all categories in y-axis variable" /> <param argument="order_xaxis" type="text" value="" optional="true" label="Type in a list of categories to order to x-axis" help="Optional. Comma delimited. Default ordering is alphabetical" /> <param argument="order_yaxis" type="text" value="" optional="true" label="Type in a list of categories to order to y-axis" help="Optional. Comma delimited. Default ordering is alphabetical" /> + <param argument="matplotlib_cmap" type="select" label="Matplotlib colormap to use for y-axis categories" help="See link below for colormaps explanation"> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="Paired">Paired</option> + <option value="Accent">Accent</option> + <option value="Dark2">Dark2</option> + <option selected="true" value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="tab10">tab10</option> + <option value="tab20">tab20</option> + <option value="tab20b">tab20b</option> + <option value="tab20c">tab20c</option> + </param> </section> </when> <when value="voronoi"> @@ -97,16 +111,9 @@ <![CDATA[ **What it does** -This tool does various single cell spatial analyses with Scimap. - -**Input** +This tool creates stacked barplots or Voronoi plots from single-cell spatial data using Scimap -AnnData. - -**Output** - -Anndata with a corresponding key added. - +For the stacked barplot tool, find colormap descriptions here: https://matplotlib.org/stable/users/explain/colors/colormaps.html ]]> </help>