Dashes to dashes, dots to dots: fine-tuning small-data graphics in R

Panels

1

Elements

3 rows: an open diamond on a horizontal line segment; a 5-marker summary in which small gray end dots are joined by dashed lines to medium gray dots, which are joined by a thick solid line through a large black dot; and 7 separate markers (2 black filled circles, 2 gray filled circles, 2 open circles, 1 X). Each row carries a blue text label

Horizontal

Log scale, 0.1 to 10, labeled Dimension 1 axis and label; dotted vertical reference line at 1

Vertical

3 unlabeled rows without ticks; axis title Dimension 2 label

Visible pattern

The interval row spans, with the diamond near 2.2. The 5-number summary spans about 0.1 to 2.1, its thick segment about 0.18 to 0.95 and its large dot near 0.45. The repeated measures spread from about 0.75 to about 7, the marker fills lightening from black through gray to open from left to right, ending in the X.

Text in the picture

Interval: 99% CI for mean
Distribution: 5-number summary
Repeated measures
Dimension 2 label
Dimension 1
axis and label

A wide table in black type fills the middle of the slide. A red arrow runs from the red label at upper left down to the Sites column heading; a second red arrow runs from the red label at upper right down to the Difference column of the right half of the table.

Text in the picture (summary)

A table of 2-month culture conversion percentages and counts for control and treatment arms, with differences and 95% confidence intervals, by study and site, for solid and liquid media.

Panels

2

Elements

Open circles with horizontal intervals: 11 in the solid media panel and 10 in the liquid media panel (the last row has none); circles vary in size, larger in rows with larger numbers in parentheses

Horizontal

-60 to 60 in each panel, panels labeled Solid media and Liquid media; dashed vertical reference line at 0

Vertical

11 rows in 4 groups: an overall row with 3 site rows, an overall row with 4 site rows, and 2 single rows; site rows indented

Visible pattern

In both panels most intervals cross the dashed line at 0, and the points lie between about -12 and 25. The overall rows have the narrowest intervals, about 20 points wide; site rows with small numbers in parentheses have the widest, reaching about 90 points. In the solid media panel the last row's interval lies just to the right of 0. Points in the liquid panel sit at or right of 0 more often than in the solid panel.

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Culture negativity at 2 months in 4 phase-2 trials:
percentage difference between moxifloxacin and control
TBTC27—Overall (277)
N America (102)
Uganda (147)
S Africa (28)
TBTC28—Overall (327)
N America (84)
Brazil (19)
Uganda (181)
S Africa (31)
Oflotub—S Africa (94)
JHU—Brazil (133)
Pointwise 95% confidence intervals with continuity correction

Panels

2

Elements

Left panel: per row up to 4 markers (filled circle, filled square, open circle, open square, per the legend), 42 in all (the last row has only the 2 filled markers), each joined to 0 by a light gray horizontal line; row sizes printed between labels and panel. Right panel: per row a filled and an open triangle with horizontal intervals, 21 in all (the last row has only the filled triangle)

Horizontal

Left panel: Percentage, 0 to 100, -60 to 60, dashed vertical reference line at 0

Vertical

11 rows in 4 groups, as on the previous slide, with site rows indented

Visible pattern

In the left panel the filled (solid medium) markers cluster mostly between about 65 and 95, while the open (liquid) markers spread more widely, from about 35 to 95. In the right panel each row's pair of triangles lies near or across 0, with points between about -12 and 25; the intervals are narrowest for the overall rows and widest for rows with small sizes, reaching from about -50 to beyond 60.

Text in the picture

Culture negativity at 2 months in 4 phase-2 trials
of moxifloxacin v control
mfx on solid
control on solid
difference on solid
mfx on liquid
control on liquid
difference on liquid
TBTC27—Overall 277
N America 102
Uganda 147
S Africa 28
TBTC28—Overall 327
N America + Spain 84
Brazil 19
Uganda 181
S Africa 31
Oflotub—S Africa 94
JHU—Brazil 133

Panels

2, titled United States and United Kingdom

Elements

Small squares with horizontal intervals, about 57 in the United States panel and 24 in the United Kingdom panel; 4 open diamonds with intervals in each panel mark summary rows; 2 intervals in the United States panel end in arrows beyond the axis, one at each end

Horizontal

Log scale, 0.05 to 20 in each panel, shared label Odds ratio; dotted vertical reference line at 1

Vertical

4 labeled groups in each panel: Discordant UAI, # Male sex partners, Receptive UAI, HIV+ status, each a list of study rows; the United States groups end in a row labeled Summary; group labels repeated at right for the United Kingdom panel

Visible pattern

In the United States panel the rows within each group are ordered by increasing point estimate, so each group slants from upper left to lower right. Discordant UAI spans about 0.15 to 2.7 and Receptive UAI about 0.45 to 2.5, both with summaries near 1; # Male sex partners lies entirely below 1, about 0.35 to 0.85, with summary near 0.6; HIV+ status lies entirely above 1, about 1.6 to 10, with summary near 3. In the United Kingdom panel the groups are shorter and closer to 1: # Male sex partners and Receptive UAI cluster between about 0.55 and 1.2, Discordant UAI between about 1 and 3, and HIV+ status mostly between about 1.4 and 2.3, with one row near 0.45 on a very wide interval.

Text in the picture (summary)

Row labels name the studies in each group by first author or survey name and year.

Panels

1

Elements

31 open circles with horizontal intervals

Horizontal

Log scale, 0.2 to 20, labeled Odds ratio; dotted vertical reference line at 1

Vertical

31 numbered categories, listed top to bottom

Visible pattern

The circles descend steadily from about 12 at the top to about 0.37 at the bottom, forming a band slanting from upper right to lower left. Interval widths vary a great deal, from very short to spanning a factor of 10.

Text in the picture

1. Black partners
2. Current STI dx
3. Undiagnosed HIV (HIV+ MSM)
4. Lower education
5. CD4 < 200 (HIV+ MSM)
6. Low income
7. Crack cocaine
8. HIV status nondisclosure (HIV+ MSM)
9. Ever incarcerated
10. No health coverage (HIV+ MSM)
11. Less ART adherence (HIV+ MSM)
12. Not virally suppressed (HIV+ MSM)
13. Childhood sex abuse
14. Less ART access (HIV+ MSM)
15. Early sex debut
16. Fewer clinical visits (HIV+ MSM)
17. Older partners
18. Unemployment
19. Concurrent partners
20. Receptive UAI
21. Serodiscordant UAI (HIV- MSM)
22. HIV+ partners (HIV- MSM)
23. Serodiscordant UAI (HIV+ MSM)
24. Injection drugs
25. Circumcised
26. 1 vs. >1 lifetime HIV tests
27. Same race partners
28. Drug use before/during sex
29. Gay ID
30. Amphetamines
31. Amyl nitrites
Odds ratio

A table fills the slide, with a caption above and footnotes below. Four large red labels with red arrows are laid over it.

Text in the picture (summary)

A table of adjusted odds ratios with 95% confidence intervals for four clinical presentations, by skin-test induration size within four HIV status and birthplace groups.

Panels

1

Elements

48 markers with vertical intervals: 4 groups, each with 4 clusters of 3 markers; marker shape and shade by clinical manifestation per the legend (black circles, dark diamonds, gray downward triangles, light upward triangles); the 3 markers in a cluster correspond to 3 induration sizes

Horizontal

4 categories: HIV+/US, HIV+/FB, HIV-/US, HIV-/FB

Vertical

Log scale, 0.1 to 5.0, labeled Odds ratio with 95% confidence interval; dashed horizontal reference line at 1.0

Visible pattern

Miliary markers (black circles) lie at or below 1 in every group. Cavitary pulmonary markers (light triangles) lie above 1 in the first 3 groups. Extrapulmonary-only markers stay between about 0.8 and 1.3, and pulmonary and extrapulmonary diamonds lie below 1 except one near 1.1 in HIV-/US.

Text in the picture

Clinical manifestation
Miliary
Pulmonary and extrapulmonary
Extrapulmonary only
Cavitary pulmonary
Noncavitary pulmonary (referent)
5-9 mm
10-14 mm
≥ 15 mm

Panels

1

Elements

16 vertical summaries, 2 per age group (circles for foster children, diamonds for biologic children, per the legend): each a large central marker on a solid segment between 2 small markers, with dotted lines extending beyond; number per subgroup printed beneath each summary

Horizontal

8 categories, Age group (years): 0-1, 2-3, 4-5, 6-7, 8-9, 10-11, 12-13, 14-16

Vertical

Weight gain (kg/mo), -1.0 to 2.0, scale repeated on left and right

Visible pattern

The central markers rise from about 0.1 to 0.45 in the youngest groups to about 0.65 in the oldest. The spreads widen with age: in the youngest groups the dotted extents stay within about -0.35 to 0.75, while in the older groups they reach from about -0.9 to about 2.1. In many groups the lower small marker sits at 0.0. From age 4-5 on, the foster and biologic central markers in each group sit close together, the biologic summaries usually spreading wider.

Text in the picture

Foster children
Biologic children
12 88 42 105 92 148 112 159 123 110 105 113 128 105 96 64

Panels

1

Elements

7 pairs of vertical lines, each line with a large central marker and small end markers; circles for women with HIV (n=369), squares for women at risk of HIV (n=184), per the legend

Horizontal

7 categories: Vitamin C, Vitamin E, Alpha carotene, Beta carotene, Lycopene, Beta cryptoxanthin, Lutein/zeaxanthin, each with a circle line on the left and a square line on the right

Vertical

NHANES centile, 0 to 100, labeled on both left and right axes; dashed gray reference lines at 25, 50 and 75; data extend from about 4 to 68, where the panel label and legend sit

Visible pattern

All 14 lines sit in the lower 2-thirds of the scale: lower ends fall between about 4 and 14, upper ends between about 34 and 68. The central markers lie between about 16 and 37, below the 50 line throughout. The 2 vitamin pairs on the left have the highest circle centers and the tallest circle lines; across the 5 categories to the right, the square line reaches higher than the circle line, and its central marker sits higher.

Text in the picture

Antioxidant levels
Women with HIV (n=369)
Women at risk of HIV (n=184)
NHANES centile

Panels

1

Elements

9 pairs of vertical lines, each line with a large central marker and small end markers; circles for women with HIV (n=369), squares for women at risk of HIV (n=184), per the legend

Horizontal

9 categories: Vitamin A, Vitamin B12, Serum folate, RBC folate, Ferritin, Iron, TIBC, Selenium, Zinc, each with a circle line on the left and a square line on the right

Vertical

NHANES centile, 0 to 100, labeled on both left and right axes; dashed gray reference lines at 25, 50 and 75; data extend from about 3 to 90

Visible pattern

The lines are long,, and together they cover nearly the whole scale, from about 3 to 90. The central markers form a rough arch across the categories: low for Vitamin A (about 26 to 30), high from Vitamin B12 through Ferritin (about 45 to 72, the Ferritin circle highest), then falling through Iron and TIBC to the lowest values for Selenium and Zinc (about 12 to 29). Within pairs the circle and square lines overlap widely.

Text in the picture

Folate and mineral levels
Women with HIV (n=369)
Women at risk of HIV (n=184)
NHANES centile

Panels

5 stacked bands of different heights, sharing one horizontal axis, each with its own vertical scale

Elements

in each band, 6 vertical summaries, one per fiscal year: a gray vertical line, thicker in its middle part, carrying dots of 3 sizes (largest near the middle, smallest at the ends); in some years an x at the top of the band. Colors by band: OMB maroon, HHS blue, CDC-OD green, CDC-NC orange, FRN red; HHS and FRN summaries are compact clusters of dots

Horizontal

Fiscal year stage was entered, 6 categories, 2004 to 2009

Vertical

Duration in stage (days), labeled on the left only, with an unlabelled mirrored tick axis on the right. OMB, CDC-OD and CDC-NC bands each have ticks labeled 91, 182 and 273 (273 at the band top); the narrow HHS band is labeled 42 at its top; the narrow FRN band is labeled 56 at its top and 0 at its bottom; other band bottoms are unlabelled

Visible pattern

OMB summaries are similar from year to year, centered near 91 days. HHS clusters sit tightly every year, and FRN clusters sit tightly near the bottom of theirs. CDC-OD centers are low in 2004, high in 2005 to 2007, and low again in 2008 and 2009. CDC-NC centers stay low while the lines stretch upward, to about 210 in 2004 and 2005 and to the x at the band top from 2006 to 2009.

Text in the picture

OMB
HHS
CDC-OD
CDC-NC
FRN
Duration in stage (days)
Fiscal year stage was entered

Panels

5 stacked bands of different heights, sharing one horizontal axis, each with its own vertical scale

Elements

in each band, a solid colored curve between 2 dotted curves of the same color, over 6 gray vertical summaries (line with dots of 3 sizes) placed about midway through each year, and gray x marks at the band top in some years. Colors by band: OMB maroon, HHS blue, CDC-OD green, CDC-NC orange, FRN red

Horizontal

Date stage was entered, 2003-10 to 2009-10, labels yearly, minor ticks monthly

Vertical

Duration in stage (days), same scales as the previous slide: OMB, CDC-OD and CDC-NC bands labeled 91, 182, 273; HHS labeled 42 at its top; FRN labeled 56 at its top and 0 at its bottom; unlabelled mirrored tick axis on the right

Visible pattern

The OMB curve runs near 90 to 110 days, rises to a peak of about 140 in mid-2008 and falls to about 75 by 2009-10. The HHS curve is nearly flat. The CDC-OD curve rises from about 65 in late 2003 to a broad peak of about 165 near 2005-10, declines to about 65 by early 2008 and stays low. The CDC-NC curve, rises to about 110 around 2006-04 and then holds near 90 to 100. The FRN curve stays low and nearly flat, with a slight rise from 2005 to 2007. The dotted curves stay close to the solid ones, separating most around the peaks.

Text in the picture

OMB
HHS
CDC-OD
CDC-NC
FRN
Duration in stage (days)
Date stage was entered

Panels

1

Elements

6 stacked smooth bands, top to bottom maroon, blue, green, orange, gray and red, separated by thin white lines; no labels or legend

Horizontal

Date stage was entered, 2003-10 to 2009-10, labels yearly, minor ticks monthly

Vertical

Time-in-process index (days), 0 to 455, ticks labeled 0, 91, 182, 273, 364, 455; unlabelled mirrored tick axis on the right; the stack reaches the top of the scale at its peak

Visible pattern

The top edge of the stack starts near 300 at 2003-10, climbs to a peak near 455 around early 2006, eases to about 380 through 2007 and 2008, and falls to about 310 at 2009-10. The green band changes most: thin (about 60) in 2003, widest (about 160) around 2006, and narrowing to about 60 by late 2008. The orange band widens from about 55 to about 110 around 2005-10 and stays wide. The red, gray and blue bands stay thin and nearly constant, and the maroon top band is about 80 to 140 thick,.

A wide typeset table fills the slide. Three red arrows run from the overlaid red labels up to column headings: one to the cancer type heading, one to the time from enrollment to cancer diagnosis heading, and one to the survival status heading. The table rows behind the red labels are faded.

Text in the picture (summary)

A typeset table listing cancer site, type, stage, timing, treatment and outcome for each of 26 women with HIV, in two groups of 14 and 12.

Panels

2, side by side, sharing row labels

Elements

left panel: 26 dashed lines from 0, each ending in an open square; right panel: 26 dashed lines from 0, each ending in a filled circle (Death) or open circle (Withdrawal), 19 filled and 7 open

Horizontal

left: Enrollment to diagnosis, 0 to 72 months, ticks every 12, one square beyond the axis end near 78; right: Diagnosis to death or withdrawal, 0 to 60 months, ticks every 12; shared title Time (months)

Vertical

26 rows in 2 labeled groups: AIDS-defining (14 rows) and Non-AIDS-defining (12 rows), each row labeled by cancer site or type

Visible pattern

In the left panel the dashed lines range from about 5 to 78 months; the 5 cervix rows are all short (about 7 to 15). In the right panel, the NHL rows end in deaths within about 9 months of diagnosis, several at or near 0, and the 4 lung rows also end in deaths within about 7 months. Withdrawals (open circles) fall late, mostly between about 42 and 64 months, except one at 0 in the last row.

Text in the picture

AIDS-defining
Kaposi's sarcoma
NHL (CNS)
NHL (CNS)
NHL (CNS)
NHL (CNS)
NHL (lung)
NHL (lung)
NHL (pleura)
NHL (tonsil)
Cervix
Cervix
Cervix
Cervix
Cervix
Non-AIDS-defining
Lung
Lung
Lung
Lung
Larynx
Bone marrow
Hand
Neck
Breast
Breast
Endometrium
Skin (basal)
Death
Withdrawal
Enrollment to
diagnosis
Diagnosis to
death or withdrawal
Time (months)

Panels

1

Elements

26 dashed lines, each running from an open square at negative time through 0 to a filled circle (Death) or open circle (Withdrawal) at positive time; 19 filled, 7 open; solid vertical line at 0

Horizontal

Time (months), -72 to 72, ticks every 12; the left half labeled Enrollment to diagnosis, the right half Diagnosis to death or withdrawal; one square beyond the left axis end near -79

Vertical

26 rows in 2 labeled groups: AIDS-defining (14 rows) and Non-AIDS-defining (12 rows), each row labeled by cancer site or type

Visible pattern

Squares spread from about -5 to -79 months, the 5 cervix rows clustered close to 0 (about -7 to -15). To the right of 0, the NHL and lung rows stop short, with deaths within about 9 months, while the cervix rows and several non-AIDS-defining rows stretch far right, to withdrawals between about 42 and 64 months. The last row ends in a withdrawal at 0 after the longest leftward line.

Text in the picture

AIDS-defining
Kaposi's sarcoma
NHL (CNS)
NHL (CNS)
NHL (CNS)
NHL (CNS)
NHL (lung)
NHL (lung)
NHL (pleura)
NHL (tonsil)
Cervix
Cervix
Cervix
Cervix
Cervix
Non-AIDS-defining
Lung
Lung
Lung
Lung
Larynx
Bone marrow
Hand
Neck
Breast
Breast
Endometrium
Skin (basal)
Death
Withdrawal
Enrollment to
diagnosis
Diagnosis to
death or withdrawal
Time (months)

Panels

1

Elements

circles in 3 fills on 26 rows: open (Normal), gray (ASCUS), black (SIL+), per the legend; dashed gray vertical reference line at 0

Horizontal

Time difference from hysterectomy (years), -6 to 6, ticks every year; data from about -5.8 to 5.9; dashed vertical guide at 0

Vertical

26 unlabeled rows in 2 bracketed groups, 19 above and 7 below, group labels rotated; legend inside the upper left

Visible pattern

In the upper group (CIN present), the rows shift leftward going down: the top rows run from about -1 to 5 years and the bottom rows from about -6 to about 0.5. In that group black and gray dots are dense to the left of zero, though some upper rows have black and gray dots out to about 4 years. In the lower group the rows together span about -4 to 6 years and nearly every dot is white, with a few gray dots in one row between about -3.5 and -1.5.

Text in the picture

Normal
ASCUS
SIL+
CIN present (n=19)
CIN absent (n=7)
Time difference from hysterectomy (years)

Panels

1

Elements

33 rows of point markers, one row per participant, without connecting lines: filled black circles, open circles, open orange upward triangles (some with a filled circle inside), open red downward triangles, and plus signs at the right margin; 6 markers ringed in orange, each with a rotated orange label; no legend

Horizontal

Days from start of therapy, −28 to 392, ticks every 28, labeled at −28, 0, 28, 56, 84, 112, 168, 224, 280, 336 and 392; a dotted gray vertical line at 0 and a dashed gray vertical line at 112; plus signs just beyond 392

Vertical

Participant ID (redacted), 33 rows, one per participant, labeled [participant IDs]; no axis line

Visible pattern

Filled circles sit near 0 in almost every row, a few up to about 30 days earlier. Orange upward triangles form a loose column between about 10 and 75 days. The red downward triangles step from about 300 days in the top row to a long column near 170 to 200 through the middle rows, then to about 75 to 115 in the bottom 6 rows. Open circles continue at roughly regular intervals to about 390 days, and plus signs end about 20 rows at the right margin. The 6 ringed markers lie between about 100 and 330 days, all but one to the right of the red triangle in their row; 5 labels read Relapse? and one reads Failure?.

Text in the picture

Participant ID (redacted)
Relapse?
Relapse?
Relapse?
Failure?
Relapse?
Relapse?
Days from start of therapy

Panels

1

Elements

27 rows, one per participant, each with up to 3 horizontal line segments in the legend's 3 styles (thin light gray, thick gray, dashed light gray), carrying 5 kinds of markers per the legend: circled plus, small filled circle, small open circle, asterisk and x; an 8-entry legend at upper right (3 line styles, 5 markers)

Horizontal

Days since start of tuberculosis therapy, −30 to 390, labeled every 30; data from about −45, with dashed follow-up lines running to the right edge, just past 390; no reference lines

Vertical

Participant index, 27 rows numbered 1 to 27 from the top, in 4 labeled sections of 8, 2, 15 and 2 rows

Visible pattern

Thin lines start at 0 in nearly every row, and thick lines take over between about 30 and 70 days and end between about 70 and 200. Dashed lines end between about 100 and 250 days in the top section and run to the right edge in most rows below. Filled circles cluster at and to the left of 0, and open circles fall along the lines at roughly regular intervals. Asterisks lie between about 70 and 175 days, mostly in the first and third sections; x marks appear in 3 rows between about 70 and 125; circled plus signs appear in 3 rows, near 120 and 325 days.

Text in the picture

Incomplete treatment, incomplete follow-up < 6 months
Incomplete treatment, incomplete follow-up ≥ 6 months
Incomplete treatment, complete follow-up
Complete treatment, late positive culture
Prestudy treatment
Study treatment
Follow-up
Treatment failure/relapse
Other positive culture
Negative culture
Hepatic adverse event
Nonhepatic adverse event
Participant index
Days since start of tuberculosis therapy

Text in the picture (summary)

A typeset table of clinical features, regimens and comments for each participant who discontinued study treatment because of adverse events, grouped by hepatic and non-hepatic events.

Panels

1

Elements

Squares in a grid, 1 per cell, filled black or hollow, and x marks; many cells blank; no legend.

Horizontal

54 columns, evenly spaced, with rotated coded labels in 9 groups of 6 by prefix, from left: gsasp, strng, inspt, npasp, stool, urine, blood, fnasp, cdrc. In the first 8 groups the labels run fm, xp, mg, each with the suffixes _1 and _2; the cdrc group has xp only, as cdrc1 to cdrc3, each with _1 and _2.

Vertical

25 rows, one per child, each labeled at left with [participant IDs]; evenly spaced, no grouping.

Visible pattern

Hollow squares fill most of the first 6 groups of columns. A few rows are mostly filled squares across those groups, and filled squares are scattered through the other rows. Several rows hold marks only in every other column over part of their width, and 1 row near the bottom is blank except for 3 filled squares. The blood group holds marks in only 1 column, mostly hollow squares with a few x marks, down the lower two-thirds of the rows; the fnasp group holds marks in only 2 rows. The cdrc group holds marks in most rows from the 2nd to about the 21st, and none in the bottom 4. X marks are few and scattered.

Text in the picture (summary)

Rows labeled with numbers; 54 columns labeled with rotated coded variable names.

Panels

1

Elements

Circles set side by side in pairs, up to 2 per column position, each filled black, hollow, or smaller and light gray; many positions blank or holding a single circle; no legend.

Horizontal

27 column positions with rotated coded labels, in 3 blocks set apart by wider gaps and marked by brackets labeled FM (8 positions), Xpert (11) and MGIT (8). In each block the specimens run gsasp, npasp, inspt, strng, stool, urine, blood, fnasp; the Xpert block adds cdrc1, cdrc2 and cdrc3 between stool and urine.

Vertical

25 rows, one per child, each labeled at left with [participant IDs]; evenly spaced, no grouping.

Visible pattern

Filled circles concentrate in the top rows of all 3 blocks and thin out downward; the lower rows are mostly hollow circles. In the FM block, filled circles appear only in the top 5 rows and 2 rows further down. The Xpert block is dense with filled circles through about the 9th row, with scattered filled circles below. In the MGIT block, filled circles reach further, through about the 18th row, and are scattered below; nearly all the gray circles are here. In FM the blood and fnasp positions are empty, and in Xpert the blood position is empty; the fnasp positions of Xpert and MGIT hold marks in only 2 rows, and the blood position of MGIT holds single circles in about half the rows. Several rows hold single circles rather than pairs, and 1 row is blank except for a single filled circle in each block.

Text in the picture (summary)

Column labels are coded variable names for specimen type and test; row labels are participant numbers.