malariagen_data.af1.Af1.plot_pca_coords_3d#

Plot sample coordinates from a principal components analysis (PCA) as a plotly 3D scatter plot.

Parameters#

dataDataFrame: A dataframe of projections along principal components, one row per sample. The columns are: sample_id is the identifier of the sample, partner_sample_id is the identifier of the sample used by the partners who contributed it, contributor is the partner who contributed the sample, country is the country the sample was collected in, location is the location the sample was collected in, year is the year the sample was collected, month is the month the sample was collected, latitude is the latitude of the location the sample was collected in, longitude is the longitude of the location the sample was collected in, sex_call is the sex of the sample, sample_set is the sample set containing the sample, release is the release containing the sample, quarter is the quarter of the year the sample was collected, study_id* is the identifier of the study the sample set containing the sample came from, `study_url is the URL of the study the sample set containing the sample came from, terms_of_use_expiry_date is the date the terms of use for the sample expire, terms_of_use_url is the URL of the terms of use for the sample, unrestricted_use indicates whether the sample can be used without restrictions (e.g., if the terms of use of expired), mean_cov is mean value of the coverage, median_cov is the median value of the coverage, modal_cov is the mode of the coverage, mean_cov_2L is mean value of the coverage on 2L, median_cov_2L is the median value of the coverage on 2L, mode_cov_2L is the mode of the coverage on 2L, mean_cov_2R is mean value of the coverage on 2R, median_cov_2R is the median value of the coverage on 2R, mode_cov_2R is the mode of the coverage on 2R, mean_cov_3L is mean value of the coverage on 3L, median_cov_3L is the median value of the coverage on 3L, mode_cov_3L is the mode of the coverage on 3L, mean_cov_3R is mean value of the coverage on 3R, median_cov_3R is the median value of the coverage on 3R, mode_cov_3R is the mode of the coverage on 3R, mean_cov_X is mean value of the coverage on X, median_cov_X is the median value of the coverage on X, mode_cov_X is the mode of the coverage on X, frac_gen_cov is the faction of the genome covered, divergence is the divergence, contam_pct is the percentage of contamination, contam_LLR is the log-likelihood ratio of contamination, aim_species_fraction_arab is the fraction of the gambcolu vs. arabiensis AIMs that indicated arabiensis (this column is only present for Ag3), aim_species_fraction_colu is the fraction of the gambiae vs. coluzzii AIMs that indicated coluzzii (this column is only present for Ag3), aim_species_fraction_colu_no2l is the fraction of the gambiae vs. coluzzii AIMs that indicated coluzzii, not including the chromosome arm 2L which contains an introgression (this column is only present for Ag3), aim_species_gambcolu_arabiensis is the taxonomic group assigned by the gambcolu vs. arabiensis AIMs (this column is only present for Ag3), aim_species_gambiae_coluzzi is the taxonomic group assigned by the gambiae vs. coluzzii AIMs (this column is only present for Ag3), aim_species_gambcolu_arabiensis is the taxonomic group assigned by the combination of both AIMs analyses (this column is only present for Ag3), country_iso is the ISO code of the country the sample was collected in, admin1_name is the name of the first administrative level the sample was collected in, admin1_iso is the ISO code of the first administrative level the sample was collected in, admin2_name is the name of the second administrative level the sample was collected in, taxon is the taxon assigned to the sample by the combination of the AIMs analysis and the cohort analysis, cohort_admin1_year is the cohort the sample belongs to when samples are grouped by first administrative level and year, cohort_admin1_month is the cohort the sample belongs to when samples are grouped by first administrative level and month, cohort_admin1_quarter is the cohort the sample belongs to when samples are grouped by first administrative level and quarter, cohort_admin2_year is the cohort the sample belongs to when samples are grouped by second administrative level and year, cohort_admin2_month is the cohort the sample belongs to when samples are grouped by second administrative level and month, cohort_admin2_quarter is the cohort the sample belong to when samples are grouped by second administrative level and quarter. PC? is the projection along principal component ? (? being an integer between 1 and the number of components). There are as many such columns as components, pca_fit is whether this sample was used for fitting.
xstr, optional, default: ‘PC1’: Name of variable to plot on the X axis.
ystr, optional, default: ‘PC2’: Name of variable to plot on the Y axis.
zstr, optional, default: ‘PC3’: Name of variable to plot on the Z axis.
colorstr or Mapping or None, optional: Name of variable to use to color the markers.
symbolstr or Mapping or None, optional: Name of the variable to use to choose marker symbols.
jitter_fracfloat or None, optional, default: 0.02: Randomly jitter points by this fraction of their range.
random_seedint, optional, default: 42: Random seed used for reproducible down-sampling.
widthint or None, optional, default: 900: Figure width in pixels (px).
heightint or None, optional, default: 600: Figure height in pixels (px).
marker_sizeint or float, optional, default: 5: Marker size.
color_discrete_sequenceList or None, optional: Provide a list of colours to use.
color_discrete_mapMapping or None, optional: Provide an explicit mapping from values to colours.
category_ordersList or Mapping or None, optional: Control the order in which values appear in the legend.
legend_sizing{‘constant’, ‘trace’}, optional, default: ‘constant’: Determines if the legend items symbols scale with their corresponding “trace” attributes or remain “constant” independent of the symbol size on the graph.
showbool, optional, default: True: If true, show the plot. If False, do not show the plot, but return the figure.
rendererstr or None, optional: The name of the renderer to use.
**kwargs: Passed through to px.scatter_3d().

Returns#

Figure or None: A plotly figure (only returned if show=False).