{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Note: *It may take a minute for the structures to render, please be patient.*" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# This notebook shows logo plots and interactive structure widgets.\n", "# It is set up so that it can be parameterized by papermill.\n", "# It is designed so that it can be run in appmode\n", "# (https://github.com/oschuett/appmode), and for that reason has\n", "# comments written mostly in code cells rather than Markdown." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# import Python modules\n", "\n", "import io\n", "import os\n", "\n", "from IPython.display import display, Image\n", "\n", "import matplotlib.image\n", "import matplotlib.pyplot as plt\n", "\n", "import nglview\n", "\n", "import pandas as pd\n", "\n", "import yaml\n", "\n", "from dmslogo import facet_plot\n", "from dms_struct.colorschemes import ValueToColorMap\n", "from dms_struct.struct_widget import colored_struct" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "tags": [ "parameters" ] }, "outputs": [], "source": [ "# This cell is tagged `parameters` to enable papermill parameterization\n", "# See: https://papermill.readthedocs.io/en/latest/usage-parameterize.html\n", "# Parameters set to `None` MUST be parameterized.\n", "\n", "data_csv = None # CSV file with tiday data frame to plot\n", "query_str = None # query data frame using this str to get just subset to plot\n", "mut_metric = 'mutdiffsel' # mutation-level selection metric\n", "site_metric = 'positive_diffsel' # site-level selection metric\n", "facet_col = None # column specifying each subset to plot, for instance serum or antibody\n", "isite_col = 'isite' # column specifying sites in sequential integer numbering\n", "site_col = 'site' # column specifying site number as str\n", "pdb_chain_col = 'pdb_chain' # column specifying PDB chain\n", "pdb_site_col = 'pdb_site' # column specifying PDB site\n", "zoom_col = 'zoom_site' # column indicating sites to zoom in logo and struct\n", "wildtype_col = 'wildtype' # column indicating wildtype identity at site\n", "mutation_col = 'mutation' # column indicating amino-acid mutant\n", "cmap = 'viridis' # color map\n", "\n", "# representation for structure, such as `cartoon`, `surface`, `spacefill`\n", "representation = ['surface', 'spacefill']\n", "\n", "outdir = None # output directory for structure images\n", "\n", "pdb = None # PDB ID\n", "# orientation of structure: https://github.com/arose/nglview/issues/785#issuecomment-487409212\n", "orientation = [113.5, 44.09, 180.08, 0, -185.38, 23.99, 110.97, 0,\n", " 2.63, -211.51, 50.12, 0, -34.66, 25.44, 46.9, 1]\n", "\n", "# specs for panel of structure images created as image file\n", "panel_height = None # height of panel plot\n", "panel_top = 0.9 # top margin of panel\n", "panel_wspace = 0.4 # space between subplots\n", "panel_legend_width = 0.3 # width of legend relative to subplots\n", "panel_fig = None # created panel imaged file\n", "\n", "# Do structures and logo plots have separate scales for immune selection coloring?\n", "separatescale = True" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Scale bar mapping the strength of immune selection to the colors in the structure and logo plots:" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# read the data\n", "data = pd.read_csv(data_csv)\n", "\n", "# query data if applicable\n", "if query_str:\n", " data = data.query(query_str)\n", "\n", "# get mutation-level data for logo plot plotting\n", "mut_df = (data\n", " [[facet_col, isite_col, site_col, pdb_chain_col, pdb_site_col,\n", " zoom_col, wildtype_col, mutation_col, mut_metric, site_metric]]\n", " .assign(**{site_col: lambda x: x[site_col].astype('str')})\n", " .assign(site_label=lambda x: x[wildtype_col] + x[site_col],\n", " facet_spaces=lambda x: x[facet_col].str.replace('-', ' '))\n", " )\n", "\n", "if separatescale:\n", " print('Immune selection color-scale is different for each structure:')\n", " mut_df_list = []\n", " for facet, facet_df in mut_df.groupby(facet_col, sort=False):\n", " colormapper = ValueToColorMap(0, facet_df[site_metric].max(), cmap=cmap)\n", " mut_df_list.append(facet_df.assign(color=lambda x: (x[site_metric]\n", " .apply(colormapper.val_to_color))))\n", " mut_df = pd.concat(mut_df_list)\n", "else:\n", " print(\"Immune selection color-scale is shared across structures:\")\n", " colormapper = ValueToColorMap(0, mut_df[site_metric].max(), cmap=cmap)\n", " mut_df = mut_df.assign(color=lambda x: (x[site_metric]\n", " .apply(colormapper.val_to_color)))\n", "\n", "# get site level data for structure images\n", "site_df = (mut_df\n", " [[facet_col, pdb_chain_col, pdb_site_col, zoom_col, 'color']]\n", " .drop_duplicates()\n", " )\n", "\n", "# show the scale bar\n", "fig, _ = colormapper.scale_bar(label='immune selection',\n", " orientation='horizontal',\n", " low_high_ticks_only=separatescale)\n", "display(fig)\n", "plt.close(fig)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "%%capture\n", "# `%%capture` prevents plots from being shown\n", "\n", "# get logo plots for each facet\n", "logoplots = {}\n", "for facet, facet_df in mut_df.groupby(facet_col, sort=False):\n", " if separatescale:\n", " ymax = facet_df[site_metric].max()\n", " else:\n", " ymax = mut_df[site_metric].max() \n", " assert ymax > 0\n", " dy = 0.055 * ymax # extra for y-limits\n", " fig, _ = facet_plot(facet_df,\n", " gridrow_col='facet_spaces',\n", " x_col=isite_col,\n", " show_col=zoom_col,\n", " draw_line_kwargs={'height_col': site_metric,\n", " 'xtick_col': site_col,\n", " 'ylabel': 'immune selection'},\n", " draw_logo_kwargs={'letter_col': mutation_col,\n", " 'letter_height_col': mut_metric,\n", " 'xtick_col': 'site_label',\n", " 'color_col': 'color',\n", " 'xlabel': site_col,\n", " 'ylabel': 'immune selection',\n", " 'clip_negative_heights': True},\n", " line_titlesuffix='site-level selection',\n", " logo_titlesuffix='mutation-level selection',\n", " share_ylim_across_rows=False,\n", " share_xlabel=True,\n", " share_ylabel=True,\n", " height_per_ax=2,\n", " set_ylims=(-dy, ymax + dy)\n", " )\n", " logoplots[facet] = fig" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "tags": [ "nbval-ignore-output" ] }, "outputs": [], "source": [ "# get structure widgets for each facet\n", "widgets = {}\n", "for facet, facet_df in site_df.groupby(facet_col, sort=False):\n", " w = colored_struct(pdb=pdb,\n", " prop_df=facet_df,\n", " chain_col=pdb_chain_col,\n", " site_col=pdb_site_col,\n", " representation=representation,\n", " highlight_col=zoom_col,\n", " orientation=orientation,\n", " )\n", " widgets[facet] = w" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Maps of immune selection:\n", " - The line plots show the total selection at each site.\n", " - The logo plots show selection for each mutation at key sites.\n", " - The structures show the selection at each site." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "scrolled": false, "tags": [ "nbval-ignore-output" ] }, "outputs": [], "source": [ "# show logo plots and widgets\n", "for facet, logofig in logoplots.items():\n", " print('-' * 24 + f\" {facet.replace('-', ' ')} \" + '-' * 24)\n", " display(logofig)\n", " display(widgets[facet])" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "images = {}\n", "for facet, w in widgets.items():\n", " images[facet] = w.render_image(factor=4, trim=True)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# YOU MUST WAIT FOR THE IMAGES ABOVE TO RENDER BEFORE RUNNING THE FOLLOWING CELLS" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "os.makedirs(outdir, exist_ok=True)\n", "png_files = {}\n", "for facet, image in images.items():\n", " png_file = os.path.join(outdir, f\"{facet}.png\")\n", " with open(png_file, 'wb') as f:\n", " if image:\n", " f.write(image.value)\n", " png_files[facet] = png_file" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Show all structures in a panel.\n", "# Follow basic idea here to show PNGs as matplotlib plot:\n", "# https://stackoverflow.com/a/50569248\n", "\n", "mpimages = {}\n", "for facet, png in png_files.items():\n", " with open(png, 'rb') as f:\n", " contents = f.read()\n", " if contents:\n", " mpimages[facet] = matplotlib.image.imread(png)\n", " else:\n", " dummyfig = plt.figure(figsize=(panel_height, panel_height))\n", " plt.xticks([], fig=dummyfig)\n", " plt.yticks([], fig=dummyfig)\n", " plt.text(0.5, 0.5,\n", " f\"Empty PNG for {facet}.\\n\"\n", " 'Did you allow widgets to render\\n'\n", " 'before running subsequent cells?',\n", " va='center', ha='center')\n", " with io.BytesIO() as f:\n", " dummyfig.savefig(f, format='png')\n", " f.seek(0)\n", " mpimages[facet] = matplotlib.image.imread(f)\n", " plt.close(dummyfig)\n", "\n", "aspects = [img.shape[1] / img.shape[0] for img in mpimages.values()]\n", "aspects.insert(0, sum(aspects) / len(aspects) * panel_legend_width * 0.5)\n", "nax = len(aspects)\n", "figwidth = panel_height * sum(aspects) * (1 + panel_wspace)\n", "avgpanelwidth = sum(aspects) / len(aspects) * panel_height\n", "\n", "fig, axes = plt.subplots(\n", " nrows=1,\n", " ncols=nax,\n", " figsize=(figwidth, panel_height),\n", " gridspec_kw={'width_ratios': aspects},\n", " )\n", "\n", "fig.subplots_adjust(left=0.5 * panel_legend_width / sum(aspects),\n", " right=1 - panel_wspace * avgpanelwidth / figwidth,\n", " bottom=0.03, top=panel_top,\n", " wspace=panel_wspace, hspace=0)\n", "\n", "_ = colormapper.scale_bar(label='immune selection',\n", " orientation='vertical',\n", " ax=axes[0],\n", " low_high_ticks_only=separatescale)\n", "\n", "for ax, (title, img) in zip(axes[1 : ], mpimages.items()):\n", " ax.imshow(img)\n", " ax.axis('off')\n", " if title:\n", " ax.set_title(title.replace('-', ' '),\n", " fontsize=17,\n", " verticalalignment='bottom',\n", " )\n", "\n", "os.makedirs(os.path.dirname(panel_fig), exist_ok=True)\n", "fig.savefig(panel_fig, dpi=400)\n", " \n", "plt.close(fig)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# to look at the PNG of the panel of images, uncomment the line below\n", "# display(Image(panel_fig))" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.7" }, "toc": { "base_numbering": 1, "nav_menu": 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