diff --git a/enigmatoolbox/datasets/__pycache__/base.cpython-37.pyc b/enigmatoolbox/datasets/__pycache__/base.cpython-37.pyc index ebb7008e..e310a634 100644 Binary files a/enigmatoolbox/datasets/__pycache__/base.cpython-37.pyc and b/enigmatoolbox/datasets/__pycache__/base.cpython-37.pyc differ diff --git a/enigmatoolbox/datasets/base.py b/enigmatoolbox/datasets/base.py index 1b23df74..fb95cfb1 100644 --- a/enigmatoolbox/datasets/base.py +++ b/enigmatoolbox/datasets/base.py @@ -281,7 +281,7 @@ def fetch_ahba(csvfile=None): Table of gene co-expression data, shape = (82, 15634) """ if csvfile is None: - url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes.csv' + url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes_stable.csv' return pd.read_csv(url, error_bad_lines=False) else: return pd.read_csv(csvfile, error_bad_lines=False) diff --git a/enigmatoolbox/permutation_testing/__pycache__/permutation_testing.cpython-37.pyc b/enigmatoolbox/permutation_testing/__pycache__/permutation_testing.cpython-37.pyc index 7dc8dd4d..e5a89147 100644 Binary files a/enigmatoolbox/permutation_testing/__pycache__/permutation_testing.cpython-37.pyc and b/enigmatoolbox/permutation_testing/__pycache__/permutation_testing.cpython-37.pyc differ diff --git a/enigmatoolbox/permutation_testing/permutation_testing.py b/enigmatoolbox/permutation_testing/permutation_testing.py index 149fd3ef..2a65b3b9 100644 --- a/enigmatoolbox/permutation_testing/permutation_testing.py +++ b/enigmatoolbox/permutation_testing/permutation_testing.py @@ -84,7 +84,7 @@ def centroid_extraction_sphere(sphere_coords, annotfile, ventricles=False): return centroid -def rotate_parcellation(coord_l, coord_r, nrot=100): +def rotate_parcellation(coord_l, coord_r, nrot=1000): """ Rotate parcellation (author: @saratheriver) @@ -95,7 +95,7 @@ def rotate_parcellation(coord_l, coord_r, nrot=100): coord_r : ndarray Coordinates of right hemisphere regions on the sphere, shape = (m, 3) nrot : int, optional - Number of rotations. Default is 100. + Number of rotations. Default is 1000. Returns ------- @@ -299,7 +299,7 @@ def perm_sphere_p(x, y, perm_id, corr_type='pearson', null_dist=False): return p_perm -def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=100, +def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=1000, type='pearson', null_dist=False, ventricles=False): """ Spin permutation (author: @saratheriver) @@ -315,7 +315,7 @@ def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot= parcellation_name : string, optional Parcellation name {'aparc', 'aparc_aseg'}. Default is 'aparc'. n_rot : int, optional - Number of spin rotations. Default is 100. + Number of spin rotations. Default is 1000. type : string, optional Correlation type {'pearson', 'spearman'}. Default is 'pearson'. null_dist : bool, optional @@ -390,7 +390,7 @@ def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot= return p_spin -def shuf_test(map1, map2, n_rot=100, type='pearson', null_dist=False): +def shuf_test(map1, map2, n_rot=1000, type='pearson', null_dist=False): """ Shuf permuation (author: @saratheriver) @@ -401,7 +401,7 @@ def shuf_test(map1, map2, n_rot=100, type='pearson', null_dist=False): map2 : narray, ndarray, or pandas.Series The other map to be correlated n_rot : int, optional - Number of shuffles. Default is 100. + Number of shuffles. Default is 1000. type : string, optional Correlation type {'pearson', 'spearman'}. Default is 'pearson'. null_dist : bool, optional diff --git a/enigmatoolbox/plotting/__pycache__/colormaps.cpython-37.pyc b/enigmatoolbox/plotting/__pycache__/colormaps.cpython-37.pyc index beb18263..98360516 100644 Binary files a/enigmatoolbox/plotting/__pycache__/colormaps.cpython-37.pyc and b/enigmatoolbox/plotting/__pycache__/colormaps.cpython-37.pyc differ diff --git a/enigmatoolbox/plotting/cmaps/bb_g.csv b/enigmatoolbox/plotting/cmaps/bb_g.csv new file mode 100644 index 00000000..b761e47a --- /dev/null +++ b/enigmatoolbox/plotting/cmaps/bb_g.csv @@ -0,0 +1,400 @@ +102 194 165 255 +102.768844221106 194.306532663317 165.452261306533 255 +103.537688442211 194.613065326633 165.904522613065 255 +104.306532663317 194.91959798995 166.356783919598 255 +105.075376884422 195.226130653266 166.809045226131 255 +105.844221105528 195.532663316583 167.261306532663 255 +106.613065326633 195.8391959799 167.713567839196 255 +107.381909547739 196.145728643216 168.165829145729 255 +108.150753768844 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85.9973322292931 85.9973121446264 255 84.7931338136016 84.793138296547 84.7931235845523 255 83.5663975107184 83.5664001410824 83.5663915088331 255 82.316279376646 82.3162799313097 82.316278111031 255 81.0421232119311 81.0421214635693 81.0421272012916 255 79.7447061604187 79.7447019057006 79.7447158687081 255 78.4255349407707 78.4255280146037 78.4255507446935 255 77.0861164772085 77.0861067525293 77.086138666696 255 75.727951171883 75.7279385592992 75.7279799509086 255 74.3525322405807 74.3525166879856 74.3525677280421 255 72.9613450550952 72.9613265472526 72.9613872857584 255 71.5558664917656 71.5558450498686 71.5559154172741 255 \ No newline at end of file diff --git a/enigmatoolbox/plotting/colormaps.py b/enigmatoolbox/plotting/colormaps.py index 3c2d9f76..9419e594 100644 --- a/enigmatoolbox/plotting/colormaps.py +++ b/enigmatoolbox/plotting/colormaps.py @@ -10,6 +10,20 @@ [70, 130, 180, 255], [196, 58, 250, 255]], dtype=np.uint8) +eco_kos_colors = np.array([[0, 0, 0, 255], + [126, 40, 127, 255], + [51, 104, 156, 255], + [167, 210, 140, 255], + [254, 205, 8, 255], + [255, 253, 25, 255]], dtype=np.uint8) + +spec_5_colors = np.array([[0, 0, 0, 255], + [50, 136, 189, 255], + [171, 221, 164, 255], + [235, 235, 181, 255], + [253, 174, 97, 255], + [213, 62, 79, 255]], dtype=np.uint8) + root_pth = os.path.dirname(__file__) TealRd_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'TealRd.csv')) GyRd_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyRd.csv')) @@ -17,5 +31,18 @@ GyBu_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyBu.csv')) GyBu_r_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyBu_r.csv')) +bb_r_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_r.csv')) +bb_o_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_o.csv')) +bb_g_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_g.csv')) +bb_p_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_p.csv')) + +bb_r_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_r.csv'))) +bb_o_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_o.csv'))) +bb_g_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_g.csv'))) +bb_p_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_p.csv'))) + colormaps = {'yeo7': yeo7_colors, 'TealRd': TealRd_colors, 'GyRd': GyRd_colors, - 'GyRd_r': GyRd_r_colors, 'GyBu': GyBu_colors, 'GyBu_r': GyBu_r_colors} + 'GyRd_r': GyRd_r_colors, 'GyBu': GyBu_colors, 'GyBu_r': GyBu_r_colors, + 'eco_kos': eco_kos_colors, 'bb_r': bb_r_colors, 'bb_o': bb_o_colors, + 'bb_g': bb_g_colors, 'bb_p': bb_p_colors, 'bb_r_r': bb_r_r_colors, 'bb_o_r': bb_o_r_colors, + 'bb_g_r': bb_g_r_colors, 'bb_p_r': bb_p_r_colors, 'spec_5': spec_5_colors} diff --git a/enigmatoolbox/utils/__pycache__/parcellation.cpython-37.pyc b/enigmatoolbox/utils/__pycache__/parcellation.cpython-37.pyc index 1172b217..d15b4065 100644 Binary files a/enigmatoolbox/utils/__pycache__/parcellation.cpython-37.pyc and b/enigmatoolbox/utils/__pycache__/parcellation.cpython-37.pyc differ diff --git a/enigmatoolbox/utils/parcellation.py b/enigmatoolbox/utils/parcellation.py index c6e5a21d..c1592df1 100755 --- a/enigmatoolbox/utils/parcellation.py +++ b/enigmatoolbox/utils/parcellation.py @@ -228,7 +228,7 @@ def parcel_to_surface(source_val, target_lab, mask=None, fill=0, source_lab=None if mask is not None: target_lab2 = target_lab[mask] - labs2 = map_to_labels(source_val, target_lab2, source_lab=source_lab) + labs2 = parcel_to_surface(source_val, target_lab2, source_lab=source_lab) return map_to_mask(labs2, mask, fill=fill) if source_lab is None: diff --git a/manuscript/codeSnippets/Untitled.ipynb b/manuscript/codeSnippets/Untitled.ipynb new file mode 100644 index 00000000..76aad89e --- /dev/null +++ b/manuscript/codeSnippets/Untitled.ipynb @@ -0,0 +1,428 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from enigmatoolbox.datasets import fetch_ahba, risk_genes\n", + "\n", + "# Fetch gene expression data\n", + "genes = fetch_ahba()" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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labelA1BGA1BG-AS1AACSAARSABCA6ABCB7ABCC12ABCC5ABCC8...ZNF8ZNF831ZNF845ZNF883ZNRF1ZSCAN18ZSCAN26ZSCAN31ZSCAN9ZYX
0L_bankssts0.6015800.6782720.7736120.6187980.4043000.3108590.6764920.6495390.657070...0.5577860.5793740.4896900.4781070.6174990.7170720.6030060.5816400.4276730.604982
1L_caudalanteriorcingulate0.5956110.6367610.8331830.5542230.2744120.2727250.6047150.6462920.620104...0.5242130.6560950.3869150.4778590.5310970.8157010.5816690.5299640.4145420.519334
2L_caudalmiddlefrontal0.5062210.6589520.8117660.6635920.4373780.3531230.6702230.5592860.686908...0.5809980.5360160.3912000.4626430.5304200.6396340.5580270.5299370.3941820.655353
3L_cuneus0.4363220.6561610.7877010.6509270.5201700.4193900.6292590.6646890.739321...0.6444200.4724020.3442070.3723400.5938590.5683850.6972670.6040010.5602360.746896
4L_entorhinal0.6142040.6149760.7306510.5137640.4590020.4550350.5020350.6057410.570617...0.5799520.6167300.5255450.6201530.6577570.6876720.4998800.4897460.3549150.456168
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77Rcaud0.3944550.2250600.3652510.4749750.6977540.5867270.0236070.2790430.192442...0.3741460.1312050.6501840.6144190.2521690.3716530.3295110.2783320.6455840.365695
78Rhippo0.7387580.3908430.4203280.2756430.3024110.7669680.1578080.5539150.266999...0.4942370.7764570.5932660.7497900.5206740.8313190.5584080.3830760.3748880.261280
79Rpal0.6972850.4478480.3675060.4491500.3768260.7222080.0387490.4555140.427285...0.4633400.5414990.6728380.8070440.4340260.5636690.5007540.3713970.3725960.349777
80Rput0.6198480.3189720.2712220.2838880.2736210.6702470.0489870.4848050.308294...0.4428040.5522870.6084800.7969270.4075780.5058360.2818850.4221080.2810230.224110
81Rthal0.6452020.6710910.7502690.6008410.3932810.3526360.5185190.6096290.714981...0.6143680.6247370.4899760.5495600.6248790.7385880.5660860.5325010.4033350.559198
\n", + "

82 rows × 3516 columns

\n", + "
" + ], + "text/plain": [ + " label A1BG A1BG-AS1 AACS AARS \\\n", + "0 L_bankssts 0.601580 0.678272 0.773612 0.618798 \n", + "1 L_caudalanteriorcingulate 0.595611 0.636761 0.833183 0.554223 \n", + "2 L_caudalmiddlefrontal 0.506221 0.658952 0.811766 0.663592 \n", + "3 L_cuneus 0.436322 0.656161 0.787701 0.650927 \n", + "4 L_entorhinal 0.614204 0.614976 0.730651 0.513764 \n", + ".. ... ... ... ... ... \n", + "77 Rcaud 0.394455 0.225060 0.365251 0.474975 \n", + "78 Rhippo 0.738758 0.390843 0.420328 0.275643 \n", + "79 Rpal 0.697285 0.447848 0.367506 0.449150 \n", + "80 Rput 0.619848 0.318972 0.271222 0.283888 \n", + "81 Rthal 0.645202 0.671091 0.750269 0.600841 \n", + "\n", + " ABCA6 ABCB7 ABCC12 ABCC5 ABCC8 ... ZNF8 ZNF831 \\\n", + "0 0.404300 0.310859 0.676492 0.649539 0.657070 ... 0.557786 0.579374 \n", + "1 0.274412 0.272725 0.604715 0.646292 0.620104 ... 0.524213 0.656095 \n", + "2 0.437378 0.353123 0.670223 0.559286 0.686908 ... 0.580998 0.536016 \n", + "3 0.520170 0.419390 0.629259 0.664689 0.739321 ... 0.644420 0.472402 \n", + "4 0.459002 0.455035 0.502035 0.605741 0.570617 ... 0.579952 0.616730 \n", + ".. ... ... ... ... ... ... ... ... \n", + "77 0.697754 0.586727 0.023607 0.279043 0.192442 ... 0.374146 0.131205 \n", + "78 0.302411 0.766968 0.157808 0.553915 0.266999 ... 0.494237 0.776457 \n", + "79 0.376826 0.722208 0.038749 0.455514 0.427285 ... 0.463340 0.541499 \n", + "80 0.273621 0.670247 0.048987 0.484805 0.308294 ... 0.442804 0.552287 \n", + "81 0.393281 0.352636 0.518519 0.609629 0.714981 ... 0.614368 0.624737 \n", + "\n", + " ZNF845 ZNF883 ZNRF1 ZSCAN18 ZSCAN26 ZSCAN31 ZSCAN9 \\\n", + "0 0.489690 0.478107 0.617499 0.717072 0.603006 0.581640 0.427673 \n", + "1 0.386915 0.477859 0.531097 0.815701 0.581669 0.529964 0.414542 \n", + "2 0.391200 0.462643 0.530420 0.639634 0.558027 0.529937 0.394182 \n", + "3 0.344207 0.372340 0.593859 0.568385 0.697267 0.604001 0.560236 \n", + "4 0.525545 0.620153 0.657757 0.687672 0.499880 0.489746 0.354915 \n", + ".. ... ... ... ... ... ... ... \n", + "77 0.650184 0.614419 0.252169 0.371653 0.329511 0.278332 0.645584 \n", + "78 0.593266 0.749790 0.520674 0.831319 0.558408 0.383076 0.374888 \n", + "79 0.672838 0.807044 0.434026 0.563669 0.500754 0.371397 0.372596 \n", + "80 0.608480 0.796927 0.407578 0.505836 0.281885 0.422108 0.281023 \n", + "81 0.489976 0.549560 0.624879 0.738588 0.566086 0.532501 0.403335 \n", + "\n", + " ZYX \n", + "0 0.604982 \n", + "1 0.519334 \n", + "2 0.655353 \n", + "3 0.746896 \n", + "4 0.456168 \n", + ".. ... \n", + "77 0.365695 \n", + "78 0.261280 \n", + "79 0.349777 \n", + "80 0.224110 \n", + "81 0.559198 \n", + "\n", + "[82 rows x 3516 columns]" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "genes" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "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": "3.7.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/manuscript/codeSnippets/codeSnippets_meta.ipynb b/manuscript/codeSnippets/codeSnippets_meta.ipynb index b8494cb4..3426636c 100644 --- a/manuscript/codeSnippets/codeSnippets_meta.ipynb +++ b/manuscript/codeSnippets/codeSnippets_meta.ipynb @@ -63,7 +63,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ diff --git a/matlab/scripts/ahba/fetch_ahba.m b/matlab/scripts/ahba/fetch_ahba.m index eb1bee3b..dbe80760 100644 --- a/matlab/scripts/ahba/fetch_ahba.m +++ b/matlab/scripts/ahba/fetch_ahba.m @@ -17,7 +17,7 @@ if nargin < 1 % Fetch the csv table from github and load it locally | option 1 - url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes.csv'; + url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes_stab.csv'; urlwrite(url, '.gtmp.csv'); genes = readtable('.gtmp.csv'); diff --git a/matlab/scripts/permutation_testing/centroid_extraction_sphere.m b/matlab/scripts/permutation_testing/centroid_extraction_sphere.m index 59038ba5..65e09d08 100644 --- a/matlab/scripts/permutation_testing/centroid_extraction_sphere.m +++ b/matlab/scripts/permutation_testing/centroid_extraction_sphere.m @@ -37,7 +37,8 @@ centroid = []; % initialisation of centroid array for ic = 1:colortable.numEntries % loop over parcellated structures if isempty(strfind(colortable.struct_names{ic},'unknown')) && ... - isempty(strfind(colortable.struct_names{ic},'corpus')) % exclude "unknown" structures and corpus callosum from the parcellation + isempty(strfind(colortable.struct_names{ic},'corpus')) && ... + isempty(strfind(colortable.struct_names{ic},'Background+FreeSurfer_Defined_Medial_Wall')) % exclude "unknown" structures and corpus callosum from the parcellation ind = ind + 1; % increment counter for every valid region label = colortable.table(ic,5); % ID of current parcel centroid(ind,:) = mean(sphere_coords(label_annot == label, :)); % average coordinates of all vertices within the current parcel to generate the centroid diff --git a/matlab/scripts/permutation_testing/rotate_parcellation.m b/matlab/scripts/permutation_testing/rotate_parcellation.m index c3d05893..ca18ed18 100644 --- a/matlab/scripts/permutation_testing/rotate_parcellation.m +++ b/matlab/scripts/permutation_testing/rotate_parcellation.m @@ -9,7 +9,7 @@ % Inputs: % coord_l (double array) - Coordinates of left hemisphere regions on the sphere, size = [m x 3] % coord_r (double array) - Coordinates of right hemisphere regions on the sphere, size = [m x 3] -% nrot (int, optional) - Number of rotations. Default is 100. +% nrot (int, optional) - Number of rotations. Default is 1000. % % Outputs: % perm_id (double array) - Array of permutations, size = [m x nrot] @@ -36,7 +36,7 @@ % default number of rotations if nargin < 3 - nrot = 100; + nrot = 1000; end nroi_l = size(coord_l,1); % n(regions) in the left hemisphere diff --git a/matlab/scripts/permutation_testing/shuf_test.m b/matlab/scripts/permutation_testing/shuf_test.m index 228259a9..13aed907 100644 --- a/matlab/scripts/permutation_testing/shuf_test.m +++ b/matlab/scripts/permutation_testing/shuf_test.m @@ -11,7 +11,7 @@ % map2 (double array) - The other map to be correlated % % Name/value pairs: -% n_rot (int, optional) - Number of spin rotations. Default is 100. +% n_rot (int, optional) - Number of spin rotations. Default is 1000. % type (string, optional) - Correlation type {'pearson', 'spearman'}. % Default is 'pearson'. % @@ -23,7 +23,7 @@ p = inputParser; -addParameter(p, 'n_rot', 100, @isnumeric); +addParameter(p, 'n_rot', 1000, @isnumeric); addParameter(p, 'type', 'pearson', @ischar); % Parse the input diff --git a/matlab/scripts/permutation_testing/spin_test.m b/matlab/scripts/permutation_testing/spin_test.m index bc1a5561..e99fceeb 100644 --- a/matlab/scripts/permutation_testing/spin_test.m +++ b/matlab/scripts/permutation_testing/spin_test.m @@ -15,7 +15,7 @@ % 'conte69'}. Default is 'fsa5'. % parcellation_name (string, optional) - Parcellation name {'aparc', % 'aparc_aseg'}. Default is 'aparc'. -% n_rot (int, optional) - Number of spin rotations. Default is 100. +% n_rot (int, optional) - Number of spin rotations. Default is 1000. % type (string, optional) - Correlation type {'pearson', 'spearman'}. % Default is 'pearson'. % ventricles (string, optional) - Whether ventricles are present in map1, @@ -41,7 +41,7 @@ p = inputParser; addParameter(p, 'surface_name', 'fsa5', @ischar); addParameter(p, 'parcellation_name', 'aparc', @ischar); -addParameter(p, 'n_rot', 100, @isnumeric); +addParameter(p, 'n_rot', 1000, @isnumeric); addParameter(p, 'type', 'pearson', @ischar); addParameter(p, 'ventricles', 'False', @ischar); diff --git a/matlab/scripts/surface_viewer/plot_cortical.m b/matlab/scripts/surface_viewer/plot_cortical.m index a4e26a65..d7ed436e 100644 --- a/matlab/scripts/surface_viewer/plot_cortical.m +++ b/matlab/scripts/surface_viewer/plot_cortical.m @@ -9,7 +9,7 @@ % Inputs: % data (double array) - vector of data, size = [1 x v] % -% Outputs: +% Name/value pairs: % surface_name (string, optional) - Name of surface {'fsa5', 'conte69}. % Default is 'fsa5'. % label_text (string, optional) - Label text for colorbar. Default is empty. @@ -19,6 +19,10 @@ % [min(data) max(data)]. % cmap (string, double array, optional) - Colormap name. Default is 'RdBu_r'. % +% Outputs: +% a (axes) - vector of handles to the axes, left to right, top to bottom +% cb (colorbar) - colorbar handle +% % Sara Lariviere | saratheriver@gmail.com p = inputParser; diff --git a/matlab/scripts/surface_viewer/plot_subcortical.m b/matlab/scripts/surface_viewer/plot_subcortical.m index 6a96855a..17a4e859 100644 --- a/matlab/scripts/surface_viewer/plot_subcortical.m +++ b/matlab/scripts/surface_viewer/plot_subcortical.m @@ -13,7 +13,7 @@ % L-ventricle, R-accumbens, R-amygdala, R-caudate, R-hippocampus, % R-pallidum, R-putamen, R-thalamus, R-ventricle % -% Outputs: +% Name/value pairs: % ventricles (string, optional) - If 'True' (default) shows the ventricles % (data must be size = [1 x 16]). If 'False', then ventricles are not % shown and data must be size = [1 x 14]. @@ -24,6 +24,10 @@ % [min(data) max(data)]. % cmap (string, double array, optional) - Colormap name. Default is 'RdBu_r'. % +% Outputs: +% a (axes) - vector of handles to the axes, left to right, top to bottom +% cb (colorbar) - colorbar handle +% % Sara Lariviere | saratheriver@gmail.com p = inputParser; diff --git a/matlab/scripts/useful/reorder_sctx.m b/matlab/scripts/useful/reorder_sctx.m index 610e1155..108bf4fd 100644 --- a/matlab/scripts/useful/reorder_sctx.m +++ b/matlab/scripts/useful/reorder_sctx.m @@ -23,5 +23,5 @@ data_r = data(:, new_order); end - + return \ No newline at end of file diff --git a/matlab/scripts/useful/surface_to_parcel.m b/matlab/scripts/useful/surface_to_parcel.m index 317fb70d..a48e5c7c 100644 --- a/matlab/scripts/useful/surface_to_parcel.m +++ b/matlab/scripts/useful/surface_to_parcel.m @@ -28,7 +28,7 @@ for ii = 1:length(uparcel) thisparcel = uparcel(ii); - surf2parcel(:, ii) = mean(surf_data(:, label_vector == thisparcel), 2); + surf2parcel(:, ii) = nanmean(surf_data(:, label_vector == thisparcel), 2); end end diff --git a/matlab/shared/colormaps/eco_kos.m b/matlab/shared/colormaps/eco_kos.m new file mode 100644 index 00000000..59b99caa --- /dev/null +++ b/matlab/shared/colormaps/eco_kos.m @@ -0,0 +1,17 @@ +function cm_data=eco_kos(m) +cm = [0 0 0; + 126 40 127; + 51 104 156; + 167 210 140; + 254 205 8; + 255 253 25]/255; + +if nargin < 1 + cm_data = cm; +else + hsv=rgb2hsv(cm); + cm_data=interp1(linspace(0,1,size(cm,1)),hsv,linspace(0,1,m)); + cm_data=hsv2rgb(cm_data); + +end +end \ No newline at end of file diff --git a/matlab/shared/colormaps/romaO.m b/matlab/shared/colormaps/romaO.m new file mode 100644 index 00000000..6d2fb078 --- /dev/null +++ b/matlab/shared/colormaps/romaO.m @@ -0,0 +1,267 @@ +function cm_data=romaO(m) +cm = [0.451373874666344 0.223458709918417 0.341870799965347 +0.454179360348631 0.222444238181896 0.336099154085492 +0.456964522293290 0.221583601522335 0.330427574767728 +0.459745820461505 0.220901628723239 0.324833950490025 +0.462508758064081 0.220345584246605 0.319346410115490 +0.465268902882544 0.219935742212323 0.313937787735644 +0.468025885957327 0.219680462176042 0.308619385744648 +0.470782101675561 0.219577010232285 0.303366719804345 +0.473519265726396 0.219623882296950 0.298217773730138 +0.476275351516132 0.219821369676404 0.293158159723772 +0.479024037655900 0.220171739281479 0.288183645222632 +0.481778917991479 0.220672622310684 0.283304066374103 +0.484529958777781 0.221302490266283 0.278502330945246 +0.487307940272339 0.222079022168182 0.273790013989858 +0.490078715420987 0.223040829891889 0.269166882473323 +0.492862402960593 0.224106403739438 0.264606084330161 +0.495670101286812 0.225363081959894 0.260159132801034 +0.498500152446305 0.226770027021745 0.255786059646747 +0.501335001941077 0.228325296954820 0.251528332963304 +0.504194621529517 0.229991675316682 0.247331299054301 +0.507065485813229 0.231880162811605 0.243219851754147 +0.509967957283227 0.233865786495777 0.239229391966027 +0.512896328092730 0.236049899338159 0.235333622211638 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cm_data=interp1(linspace(0,1,size(cm,1)),hsv,linspace(0,1,m)); + cm_data=hsv2rgb(cm_data); + +end +end \ No newline at end of file diff --git a/matlab/shared/colormaps/romaO_r.m b/matlab/shared/colormaps/romaO_r.m new file mode 100644 index 00000000..3ac0d221 --- /dev/null +++ b/matlab/shared/colormaps/romaO_r.m @@ -0,0 +1,268 @@ +function cm_data=romaO_r(m) +cm = [0.451373874666344 0.223458709918417 0.341870799965347 +0.454179360348631 0.222444238181896 0.336099154085492 +0.456964522293290 0.221583601522335 0.330427574767728 +0.459745820461505 0.220901628723239 0.324833950490025 +0.462508758064081 0.220345584246605 0.319346410115490 +0.465268902882544 0.219935742212323 0.313937787735644 +0.468025885957327 0.219680462176042 0.308619385744648 +0.470782101675561 0.219577010232285 0.303366719804345 +0.473519265726396 0.219623882296950 0.298217773730138 +0.476275351516132 0.219821369676404 0.293158159723772 +0.479024037655900 0.220171739281479 0.288183645222632 +0.481778917991479 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b/matlab/shared/surfstat/SurfStatDataCursor.m @@ -0,0 +1,17 @@ +function txt=SurfStatDataCursor(empt,event_obj) +pos=get(event_obj,'Position'); +h=get(event_obj,'Target'); +v=get(h,'Vertices'); +x=get(h,'FaceVertexCData'); +id1=min(find(v(:,1)==pos(1)&v(:,2)==pos(2)&v(:,3)==pos(3))); +tag=get(get(h,'Parent'),'Tag'); +[s,a,id0]=strread(tag,'%s %d %d'); +id=id1+id0 +txt = {['x: ',num2str(pos(1))],... + ['y: ',num2str(pos(2))],... + ['z: ',num2str(pos(3))],... + ['id: ',num2str(id)],... + ['value: ',num2str(x(id1))]}; +return +end +